ABCA1
Coloration (feathers)
Cholesterol metabolism
Coding,
SNP
N
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Attie AD; Hamon Y; Brooks-Wilson AR ; et al. (2002)
Identification and functional analysis of a naturally occurring E89K mutation in the ABCA1 gene of t[...]
GP00001682
Abca1
P41233
Morphology; Physiology
Morphology; Physiology
amino acid substitution at a residue that is conserved in the ABCA1 gene between human; mouse; chicken; and Takifugu rubripes. Generation of a mouse ABCA1 protein with the mutation disrupts protein function. N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
ABCA1
Gallus gallus
chicken - (species)
Published - Accepted by Curator
ABCB1
Plant size (dwarfism)
Unknown,
Unknown
Cenchrus americanus
(species)
Domesticated
Linkage Mapping
Parvathaneni RK; Jakkula V; Padi FK ; et al. (2013)
Fine-mapping and identification of a candidate gene underlying the d2 dwarfing phenotype in pearl mi[...]
GP00000006
ABCB1
Q9ZR72
Morphology
unknown
Cenchrus americanus
(species)
Cenchrus americanus
(species)
ABCB1
Cenchrus americanus
(species)
Published - Accepted by Curator
ABCB1
Plant size (dwarfism)
Coding,
Insertion
N
Sorghum bicolor
sorghum - (species)
Domesticated
Candidate Gene
Multani DS; Briggs SP; Chamberlin MA ; et al. (2003)
Loss of an MDR transporter in compact stalks of maize br2 and sorghum dw3 mutants.
GP00000007
ABCB1
Q9ZR72
Morphology
882bp direct duplication in exon 5 of the dw3 allele driving loss-of-function N
Sorghum bicolor
sorghum - (species)
Sorghum bicolor
sorghum - (species)
ABCB1
Sorghum bicolor
sorghum - (species)
Published - Accepted by Curator
ABCC2
Xenobiotic resistance (insecticide)
Coding,
Insertion
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Atsumi S; Miyamoto K; Yamamoto K ; et al. (2012)
Single amino acid mutation in an ATP-binding cassette transporter gene causes resistance to Bt toxin[...]
GP00000011
ABCC2
A0A0E3ZDK3
Physiology
1a.a. insertion at codon 234 (Tyr)
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
ABCC2
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
ABCG2
Milk yield
Coding,
SNP
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Cohen-Zinder M; Seroussi E; Larkin DM ; et al. (2005)
Identification of a missense mutation in the bovine ABCG2 gene with a major effect on the QTL on chr[...]
1 Additional References
GP00000015
Abcg2
Q7TMS5
Physiology
Tyr581Ser
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
ABCG2
Bos taurus
cattle - (species)
Published - Accepted by Curator
ABCG2
Milk yield
Unknown,
Unknown
Ovis aries
sheep - (species)
Domesticated
Candidate Gene
García-Fernández M; Gutiérrez-Gil B; Sánchez JP ; et al. (2011)
The role of bovine causal genes underlying dairy traits in Spanish Churra sheep.
GP00000016
Abcg2
Q7TMS5
Physiology
unknown
Ovis aries
sheep - (species)
Ovis aries
sheep - (species)
ABCG2
Ovis aries
sheep - (species)
Published - Accepted by Curator
AEP2
Hybrid Incompatibility (F2 sterility)
Coding,
SNP
Saccharomyces bayanus
(species)
Domesticated
Linkage Mapping
Lee HY; Chou JY; Cheong L ; et al. (2008)
Incompatibility of nuclear and mitochondrial genomes causes hybrid sterility between two yeast speci[...]
GP00000051
AEP2
P22136
Physiology
The region between aa 348 and aa 496 plays a critical role. When this region was further dissected in the constructs H-AEP2-bcb and H-AEP2-m3; both failed to restore respiration in the Chromosome 13 line. This result suggests that multiple critical mutations have occurred during the functional diversification of Sc-AEP2 and Sb-AEP2.
Exact causing mutation(s) not determined
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces bayanus
(species)
AEP2
Saccharomyces bayanus
(species)
Published - Accepted by Curator
aggrecan
Body size (dwarfism)
Coding,
Insertion
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Cavanagh JA; Tammen I; Windsor PA ; et al. (2007)
Bulldog dwarfism in Dexter cattle is caused by mutations in ACAN.
GP00002140
ACAN
P16112
Morphology
2266_2267insGGCA mutation introduces a frameshift and a premature termination codon into exon 11; the frameshift occurs at amino acid position 756 ; the termination codon occurs at position 914 compared to the normal aggrecan product of 2327 amino acids N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
aggrecan
Bos taurus
cattle - (species)
Published - Accepted by Curator
aggrecan
Body size (dwarfism)
Cis-regulatory,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Cavanagh JA; Tammen I; Windsor PA ; et al. (2007)
Bulldog dwarfism in Dexter cattle is caused by mutations in ACAN.
GP00002141
ACAN
P16112
Morphology
−198C>T transition predicted to introduce a new ATG start codon 199 bp upstream of the normal start codon N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
aggrecan
Bos taurus
cattle - (species)
Published - Accepted by Curator
aggrecan
Body size (dwarfism)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Eberth JE; Graves KT; MacLeod JN ; et al. (2018)
Multiple alleles of ACAN associated with chondrodysplastic dwarfism in Miniature horses.
GP00002142
ACAN
P16112
Morphology
g.95257458_95257500del ; p.Phe2017-Asp2023del N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
aggrecan
Equus caballus
horse - (species)
Published - Accepted by Curator
aggrecan
Body size (dwarfism)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Metzger J; Gast AC; Schrimpf R ; et al. (2017)
Whole-genome sequencing reveals a potential causal mutation for dwarfism in the Miniature Shetland p[...]
1 Additional References
GP00002143
ACAN
P16112
Morphology
g.95282140C>G ; p.Ala505Pro
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
aggrecan
Equus caballus
horse - (species)
Published - Accepted by Curator
aggrecan
Body size (dwarfism)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Eberth JE; Graves KT; MacLeod JN ; et al. (2018)
Multiple alleles of ACAN associated with chondrodysplastic dwarfism in Miniature horses.
GP00002144
ACAN
P16112
Morphology
g.95284530C>T ; p.Val424Met
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
aggrecan
Equus caballus
horse - (species)
Published - Accepted by Curator
aggrecan
Body size (dwarfism)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Eberth JE; Graves KT; MacLeod JN ; et al. (2018)
Multiple alleles of ACAN associated with chondrodysplastic dwarfism in Miniature horses.
GP00002145
ACAN
P16112
Morphology
g.95291270del ; p.Lys82fs N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
aggrecan
Equus caballus
horse - (species)
Published - Accepted by Curator
Agouti
Coloration (coat; dorso-ventral)
Cis-regulatory,
Unknown
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Drögemüller C; Giese A; Martins-Wess F ; et al. (2006)
The mutation causing the black-and-tan pigmentation phenotype of Mangalitza pigs maps to the porcine[...]
GP00000058
Asip
Q03288
Morphology
unknown
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
Agouti
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Agouti
Coloration (coat)
Cis-regulatory,
Insertion
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Girardot M; Guibert S; Laforet MP ; et al. (2006)
The insertion of a full-length Bos taurus LINE element is responsible for a transcriptional deregula[...]
GP00000059
Asip
Q03288
Morphology
LINE element insertion in 5' region of gene; over expression of alternative splice forms
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Agouti
Bos taurus
cattle - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Linkage Mapping
Eizirik E; Yuhki N; Johnson WE ; et al. (2003)
Molecular genetics and evolution of melanism in the cat family.
GP00000063
Asip
Q03288
Morphology
Deletion of nt 123-124 N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
Agouti
Felis catus
domestic cat - (species)
Published - Accepted by Curator
Agouti
Coloration (coat)
Coding,
Deletion
N
Vulpes vulpes
red fox - (species) D
Domesticated
Candidate Gene
Våge DI; Lu D; Klungland H ; et al. (1997)
A non-epistatic interaction of agouti and extension in the fox, Vulpes vulpes.
GP00000067
Asip
Q03288
Morphology
166 bp deletion in exon 1 N
Vulpes vulpes
red fox - (species)
Vulpes vulpes
red fox - (species) D
Agouti
Vulpes vulpes
red fox - (species)
Published - Accepted by Curator
Agouti
Coloration (feathers)
Coding,
Deletion
N
Coturnix japonica
Japanese quail - (species) D
Domesticated
Linkage Mapping
Hiragaki T; Inoue-Murayama M; Miwa M ; et al. (2008)
Recessive black is allelic to the yellow plumage locus in Japanese quail and associated with a frame[...]
GP00000068
Asip
Q03288
Morphology
8bp frameshift deletion N
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species) D
Agouti
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
Agouti
Coloration (feathers)
Cis-regulatory,
Deletion
Coturnix japonica
Japanese quail - (species) D
Domesticated
Linkage Mapping
Nadeau NJ; Minvielle F; Ito S ; et al. (2008)
Characterization of Japanese quail yellow as a genomic deletion upstream of the avian homolog of the[...]
1 Additional References
GP00000069
Asip
Q03288
Morphology
141162-bp deletion resulting in novel promoter sharing and expression of a RALY-ASIP fusion transcript
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species) D
Agouti
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
Agouti
Coloration (feathers)
Gene Amplification,
Insertion
Coturnix japonica
Japanese quail - (species) D
Domesticated
Linkage Mapping
Robic A; Morisson M; Leroux S ; et al. (2019)
Two new structural mutations in the 5' region of the ASIP gene cause diluted feather color phenotype[...]
GP00001973
Asip
Q03288
Morphology
71-kb tandem duplication that comprises one unchanged copy of ASIP and one copy present in the ITCH-ASIP fusion gene which leads to a transcript coding for a normal ASIP protein
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species) D
Agouti
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies)
Domesticated
Candidate Gene
Berryere TG; Kerns JA; Barsh GS ; et al. (2005)
Association of an Agouti allele with fawn or sable coat color in domestic dogs.
GP00000060
Asip
Q03288
Morphology
c.244G>T + 248G>A ; p.A82S + p.R83H
A82S and R83H in Linkage Disequilibrium
a G-to-T transversion and a G-to-A transition in exon 4 at positions corresponding to residues 244 and 248 of the cDNA sequence
It is unknown if one or both substitutions alter Agouti protein function
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies)
Agouti (ASIP)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Kerns JA; Newton J; Berryere TG ; et al. (2004)
Characterization of the dog Agouti gene and a nonagoutimutation in German Shepherd Dogs.
1 Additional References
GP00000061
Asip
Q03288
Morphology
R96C ; g.23393552C>T c.286C>T p.R96C
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
Agouti (ASIP)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Gene Amplification,
Insertion
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Norris BJ; Whan VA (2008)
A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sh[...]
1 Additional References
GP00001324
Asip
Q03288
Morphology
~190kb gene duplication causing dominant white phenotype. Duplication was facilitated by homologous recombination between two non-LTR SINE sequences flanking the duplicated segment ; possible involvement of gene conversion.
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
Agouti (ASIP)
Ovis aries
sheep - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Cis-regulatory,
SNP
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Norris BJ; Whan VA (2008)
A gene duplication affecting expression of the ovine ASIP gene is responsible for white and black sh[...]
GP00001325
Asip
Q03288
Morphology
unidentified promoter silencing
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
Agouti (ASIP)
Ovis aries
sheep - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
SNP
Equus asinus
ass - (species) D
Domesticated
Candidate Gene
Abitbol M; Legrand R; Tiret L (2015)
A missense mutation in the agouti signaling protein gene (ASIP) is associated with the no light poin[...]
GP00001335
Asip
Q03288
Morphology
c.349T>C p.Cys117Arg
Equus asinus
ass - (species)
Equus asinus
ass - (species) D
Agouti (ASIP)
Equus asinus
ass - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dreger DL; Schmutz SM (2011 Sep-Oct)
A SINE insertion causes the black-and-tan and saddle tan phenotypes in domestic dogs.
GP00001336
Asip
Q03288
Morphology
A 239bp SINE insertion in reverse orientation in intron 1
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Agouti (ASIP)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
Insertion
N
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Fontanesi L; Forestier L; Allain D ; et al. (2010)
Characterization of the rabbit agouti signaling protein (ASIP) gene: transcripts and phylogenetic an[...]
1 Additional References
GP00001968
Asip
Q03288
Morphology
an insertion in exon 2 of the black nonagouti allele = c.5_6insA mutation which causes a frameshift and a predicted truncated protein of only 21 amino acids N
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
Agouti (ASIP)
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
Deletion
N
Camelus dromedarius
Arabian camel - (species) D
Domesticated
Candidate Gene
Almathen F; Elbir H; Bahbahani H ; et al. (2018)
Polymorphisms in MC1R and ASIP Genes are Associated with Coat Color Variation in the Arabian Camel.
1 Additional References
GP00001978
Asip
Q03288
Morphology
1-bp deletion at position 23 resulting in frameshift N
Camelus dromedarius
Arabian camel - (species)
Camelus dromedarius
Arabian camel - (species) D
Agouti (ASIP)
Camelus dromedarius
Arabian camel - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Cis-regulatory,
Insertion
Mus musculus
house mouse - (species) D
Domesticated
Candidate Gene
Morgan HD; Sutherland HG; Martin DI ; et al. (1999)
Epigenetic inheritance at the agouti locus in the mouse.
GP00002107
Asip
Q03288
Morphology
insertion of an intra-cisternal A particle (IAP) retrotransposon upstream of the agouti gene (A). This activates transcription and causes ectopic expression of agouti protein; resulting in yellow fur; obesity; diabetes and increased susceptibility to tumours. The pleiotropic effects of ectopic agouti expression are presumably due to effects of the paracrine signal on other tissues.
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species) D
Agouti (ASIP)
Mus musculus
house mouse - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (skin)
Cis-regulatory,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Candidate Gene
Yu S; Wang G; Liao J (2019)
Association of a novel SNP in the ASIP gene with skin color in black-bone chicken.
GP00002130
Asip
Q03288
Morphology
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
Agouti (ASIP)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Coding,
SNP
Vicugna pacos
alpaca - (species) D
Domesticated
Candidate Gene
Chandramohan B; Renieri C; La Manna V ; et al. (2013)
The alpaca agouti gene: genomic locus, transcripts and causative mutations of eumelanic and pheomela[...]
GP00002336
Asip
Q03288
Morphology
p.R98C likely affecting conformation in a cysteine-rich domain
Vicugna pacos
alpaca - (species)
Vicugna pacos
alpaca - (species) D
Agouti (ASIP)
Vicugna pacos
alpaca - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Cis-regulatory,
Insertion
Bubalus bubalis
water buffalo - (species) D
Domesticated
Association Mapping
Liang D; Zhao P; Si J ; et al. (2021)
Genomic Analysis Revealed a Convergent Evolution of LINE-1 in Coat Color: A Case Study in Water Buff[...]
GP00002370
Asip
Q03288
Morphology
"2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene is the causative mutation for the white coat phenotype in swamp buffalo (Bubalus bubalis). This LINE-1 insertion (3′ truncated and containing only 5′ UTR) functions as a strong proximal promoter that leads to a 10-fold increase in the transcription of ASIP in white buffalo skin. The 165 bp of 5′ UTR transcribed from the LINE-1 is spliced into the first coding exon of ASIP, resulting in a chimeric transcript. The increased expression of ASIP prevents melanocyte maturation, leading to the absence of pigment in white buffalo skin and hairs. Phylogenetic analyses indicate that the white buffalo-specific ASIP allele originated from a recent genetic transposition event in swamp buffalo. Interestingly, as a similar LINE-1 insertion has been identified in the cattle ASIP gene, we discuss the convergent mechanism of coat color evolution in the Bovini tribe."
Bubalus bubalis
water buffalo - (species)
Bubalus bubalis
water buffalo - (species) D
Agouti (ASIP)
Bubalus bubalis
water buffalo - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat; dorso-ventral)
Coding,
Insertion
N
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Letko A; Ammann B; Jagannathan V ; et al. (2020)
A deletion spanning the promoter and first exon of the hair cycle-specific ASIP transcript isoform i[...]
GP00002373
Asip
Q03288
Morphology
"The structural variant represented an approximately 11 kb deletion (NC_013672.1:g.5,455,408_5,466,123del; Fig. 2). In rabbit, there are currently two ASIP transcript isoforms annotated (NCBI annotation release 102). The deletion removes the entire first 5′-untranslated exon of one of these transcripts (NM_001122939.1). (...) he deletion removed the transcription start site and the first untranslated exon of the presumably hair cycle-specific transcript isoform, suggesting that this is the most likely causative variant for the black and tan phenotype." N
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
Agouti (ASIP)
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration
Gene Amplification,
Insertion
Capra hircus
goat - (species) D
Domesticated
Association Mapping
Guo J; Sun X; Mao A ; et al. (2022)
A 13.42-kb tandem duplication at the ASIP locus is strongly associated with the depigmentation pheno[...]
GP00002380
Asip
Q03288
Morphology
"We confirmed that a genomic region harboring the ASIP gene is a major locus affecting the coat color phenotype of Swiss markings in goats. Although the molecular genetic mechanisms remain unsolved, the 13,420-bp duplication upstream of ASIP is a necessary but not sufficient condition for this phenotype in goats. Moreover, the variations in the copy number of the duplication across different goat breeds do not lead to phenotypic heterogeneity."
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
Agouti (ASIP)
Capra hircus
goat - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Gene Amplification,
Insertion
Capra hircus
goat - (species) D
Domesticated
Candidate Gene
Henkel J; Dubacher A; Bangerter E ; et al. (2021)
Introgression of ASIP and TYRP1 Alleles Explains Coat Color Variation in Valais Goats.
GP00002381
Asip
Q03288
Morphology
"The white Capra Sempione carried one copy of the AWt allele, which is commonly found in Saanen and Appenzell goats. AWt involves a triplication of ~155 kb comprising the coding sequence of the ASIP, AHCY and ITCH genes (Fontanesi et al. 2009; Henkel et al. 2019). Closer inspection of the short-read alignments revealed that the sequenced Capra Sempione had acquired additional smaller structural alterations compared to the original AWt allele, which comprised a duplication of 1053 bp inserted into a 10 194 bp deletion of the original AWt CNV allele (Supplementary Figure S1)."
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
Agouti (ASIP)
Capra hircus
goat - (species)
Published - Accepted by Curator
Agouti (ASIP)
Coloration (coat)
Gene Amplification,
Insertion
Capra hircus
goat - (species) D
Domesticated
Candidate Gene
Henkel J; Dubacher A; Bangerter E ; et al. (2021)
Introgression of ASIP and TYRP1 Alleles Explains Coat Color Variation in Valais Goats.
GP00002382
Asip
Q03288
Morphology
"The greyish Grüenochte goat carried one copy of the Apc allele, which causes the characteristic black and white pattern of Swiss Peacock goats (Henkel et al. 2019). The Apc allele consists of a central quadruplication of ~45 kb with triplicated adjacent flanking regions comprising ~28 kb and ~42 kb, respectively."
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
Agouti (ASIP)
Capra hircus
goat - (species)
Published - Accepted by Curator
AHR
Xenobiotic resistance (polycyclic aromatic hydrocarbons; TCDD)
Coding,
SNP
Mus musculus
house mouse - (species)
Domesticated
Linkage Mapping
Poland A; Palen D; Glover E (1994)
Analysis of the four alleles of the murine aryl hydrocarbon receptor.
GP00001810
Ahr
P30561
Physiology
alanine at position 375 mutated into valine; decreases the affinity 4-fold
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species)
AHR
Mus musculus
house mouse - (species)
Published - Accepted by Curator
Alk / Starch Synthase II
Grain cooking texture
4 Mutations:
Coding
SNP
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Umemoto T; Yano M; Satoh H ; et al. (2002)
Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and [...]
2 Additional References
GP00000078
SSII-3
Q0DDE3
Physiology
4 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Alk / Starch Synthase II
Oryza sativa
rice - (species)
Published - Accepted by Curator
ALMT gene cluster
Metal tolerance
Gene Amplification,
Indel
Secale cereale
rye - (species)
Domesticated
Linkage Mapping
Collins NC; Shirley NJ; Saeed M ; et al. (2008)
An ALMT1 gene cluster controlling aluminum tolerance at the Alt4 locus of rye (Secale cereale L).
GP00000079
ALMT1
Q76LB1
Physiology
Copy number Variant
Secale cereale
rye - (species)
Secale cereale
rye - (species)
ALMT gene cluster
Secale cereale
rye - (species)
Published - Accepted by Curator
ALMT1
Metal tolerance
Cis-regulatory,
Unknown
Triticum aestivum
bread wheat - (species)
Domesticated
Linkage Mapping
Raman H; Zhang K; Cakir M ; et al. (2005)
Molecular characterization and mapping of ALMT1, the aluminium-tolerance gene of bread wheat (Tritic[...]
2 Additional References
GP00000080
ALMT1
Q76LB1
Physiology
multiple regulatory changes
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species)
ALMT1
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
AMN1
Cell separation
Coding,
SNP
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Yvert G; Brem RB; Whittle J ; et al. (2003)
Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors.
GP00000082
AMN1
P38285
Physiology
D368V
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
AMN1
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
amylase
Starch processing
Gene Amplification,
Insertion
Mus musculus
house mouse - (species) D
Domesticated
Candidate Gene
Pajic P; Pavlidis P; Dean K ; et al. (2019)
Independent amylase gene copy number bursts correlate with dietary preferences in mammals.
GP00001867
Amy1
P00687
Physiology
Copy Number Variation
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species) D
amylase
Mus musculus
house mouse - (species)
Published - Accepted by Curator
amylase
Starch processing
Gene Amplification,
Insertion
Rattus norvegicus
Norway rat - (species) D
Domesticated
Candidate Gene
Pajic P; Pavlidis P; Dean K ; et al. (2019)
Independent amylase gene copy number bursts correlate with dietary preferences in mammals.
GP00001868
Amy1
P00687
Physiology
Copy Number Variation
Rattus norvegicus
Norway rat - (species)
Rattus norvegicus
Norway rat - (species) D
amylase
Rattus norvegicus
Norway rat - (species)
Published - Accepted by Curator
amylase
Starch processing
Gene Amplification,
Insertion
Sus scrofa
pig - (species) D
Domesticated
Candidate Gene
Pajic P; Pavlidis P; Dean K ; et al. (2019)
Independent amylase gene copy number bursts correlate with dietary preferences in mammals.
GP00001869
Amy1
P00687
Physiology
Copy Number Variation
Sus scrofa
pig - (species)
Sus scrofa
pig - (species) D
amylase
Sus scrofa
pig - (species)
Published - Accepted by Curator
amylase 2B (AMY2B)
Starch processing
Gene Amplification,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Axelsson E; Ratnakumar A; Arendt ML ; et al. (2013)
The genomic signature of dog domestication reveals adaptation to a starch-rich diet.
4 Additional References
GP00000086
LOC479922
L7N0N6
Physiology
Copy Number Variation
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
amylase 2B (AMY2B)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
an2-like (Stan2)
Coloration (tuber skin)
Cis-regulatory,
Unknown
Solanum tuberosum
potato - (species)
Domesticated
Linkage Mapping
Jung CS; Griffiths HM; De Jong DM ; et al. (2009)
The potato developer (D) locus encodes an R2R3 MYB transcription factor that regulates expression of[...]
GP00000088
AN2
A4GRU8
Morphology
unknown
Solanum tuberosum
potato - (species)
Solanum tuberosum
potato - (species)
an2-like (Stan2)
Solanum tuberosum
potato - (species)
Published - Accepted by Curator
anthocyanin2 (an2)
Coloration (fruit)
Cis-regulatory,
Unknown
Capsicum chinense
(species)
Domesticated
Linkage Mapping
Borovsky Y; Oren-Shamir M; Ovadia R ; et al. (2004)
The A locus that controls anthocyanin accumulation in pepper encodes a MYB transcription factor homo[...]
GP00000087
AN2
A4GRU8
Morphology
unknown
Capsicum annuum
(species)
Capsicum chinense
(species)
anthocyanin2 (an2)
Capsicum chinense
(species)
Published - Accepted by Curator
anthocyanin2 (an2)
Coloration (anthocyanin accumulation in entire plant)
Cis-regulatory,
Insertion
Capsicum annuum
(species) D
Domesticated
Candidate Gene
Jung S; Venkatesh J; Kang MY ; et al. (2019)
A non-LTR retrotransposon activates anthocyanin biosynthesis by regulating a MYB transcription facto[...]
GP00002051
AN2
A4GRU8
Morphology; Physiology
insertion of a 4.2 kb non-LTR retrotransposon in the promoter (672 bp upstream of the start codon of CaAn2) which may activate expression of CaAn2 by recruiting transcription factors at the 3' UTR
Capsicum annuum
(species)
Capsicum annuum
(species) D
anthocyanin2 (an2)
Capsicum annuum
(species)
Published - Accepted by Curator
APJ1
Xenobiotic resistance (alcohol, ethanol)
Cis-regulatory,
Unknown
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Swinnen S; Schaerlaekens K; Pais T ; et al. (2012)
Identification of novel causative genes determining the complex trait of high ethanol tolerance in y[...]
GP00000097
APJ1
P53940
Physiology
unknown
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
APJ1
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
apontic-like
Coloration (larval color pattern)
Cis-regulatory,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Yoda S; Yamaguchi J; Mita K ; et al. (2014)
The transcription factor Apontic-like controls diverse colouration pattern in caterpillars.
2 Additional References
GP00001386
apt
O61602
Morphology
233-kb region around apt-like (pS) refined as 33kb interval in apt-like Intron 1 (+p) with uncharacterized haplotype driving apt-like upregulation in derived phenotypes
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
apontic-like
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
Aquaporin (AQY1)
Growth rate (environment-dependent)
2 Mutations:
Coding
SNP
N
Saccharomyces cerevisiae
baker's yeast - (species) D
Domesticated
Linkage Mapping
Will JL; Kim HS; Clarke J ; et al. (2010)
Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisia[...]
1 Additional References
GP00001872
AQP1
P29972
Physiology
2 mutations
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species) D
Aquaporin (AQY1)
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
Aquaporin (AQY1)
Growth rate (environment-dependent)
Coding,
Deletion
N
Saccharomyces cerevisiae
baker's yeast - (species) D
Domesticated
Candidate Gene
Will JL; Kim HS; Clarke J ; et al. (2010)
Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisia[...]
1 Additional References
GP00001873
AQP1
P29972
Physiology
aquaporin yeast 1 gene on chromosome 12 - A881 deletion renders AQY1 inactive - size of the deletion not indicated in the paper - GenBank accession numbers for AQY1 and AQY2: GQ848552-74 and GQ870433-54 N
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species) D
Aquaporin (AQY1)
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
Aquaporin (AQY1)
Growth rate (environment-dependent)
Coding,
Deletion
N
Saccharomyces cerevisiae
baker's yeast - (species) D
Domesticated
Linkage Mapping
Will JL; Kim HS; Clarke J ; et al. (2010)
Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisia[...]
1 Additional References
GP00001874
AQP1
P29972
Physiology
aquaporin yeast 1 gene on chromosome 12 - 955-bp deletion that removes the first 106 bp of AQY1 and its upstream region - GenBank accession numbers for AQY1 and AQY2: GQ848552-74 and GQ870433-54 N
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species) D
Aquaporin (AQY1)
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
Aquaporin (AQY2)
Growth rate (environment-dependent)
Coding,
Deletion
N
Saccharomyces cerevisiae
baker's yeast - (species) D
Domesticated
Linkage Mapping
Will JL; Kim HS; Clarke J ; et al. (2010)
Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisia[...]
1 Additional References
GP00001875
AQP1
P29972
Physiology
aquaporin yeast 2 gene on chromosome 11 - 11-bp deletion that creates a stop codon in the middle of the AQY2 gene - GenBank accession numbers for AQY1 and AQY2: GQ848552-74 and GQ870433-54 N
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species) D
Aquaporin (AQY2)
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
Aquaporin (AQY2)
Growth rate (environment-dependent)
Coding,
Deletion
N
Saccharomyces cerevisiae
baker's yeast - (species) D
Domesticated
Candidate Gene
Will JL; Kim HS; Clarke J ; et al. (2010)
Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisia[...]
1 Additional References
GP00001876
AQP1
P29972
Physiology
aquaporin yeast 2 gene on chromosome 11 - deletion of nucleotide G at position 25 (G25) which creates a frameshift the AQY2 gene - GenBank accession numbers for AQY1 and AQY2: GQ848552-74 and GQ870433-54 N
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species) D
Aquaporin (AQY2)
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
Aquaporin (AQY2)
Growth rate (environment-dependent)
Coding,
Deletion
N
Saccharomyces cerevisiae
baker's yeast - (species) D
Domesticated
Candidate Gene
Will JL; Kim HS; Clarke J ; et al. (2010)
Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisia[...]
GP00001877
AQP1
P29972
Physiology
aquaporin yeast 2 gene on chromosome 11 - G528 deletion which creates a frameshift the AQY2 gene - tested in assays - GenBank accession numbers for AQY1 and AQY2: GQ848552-74 and GQ870433-54 N
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species) D
Aquaporin (AQY2)
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
ARHGAP15
Pathogen resistance (Trypanosoma)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Noyes H; Brass A; Obara I ; et al. (2011)
Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypa[...]
GP00000103
Arhgap15
Q811M1
Physiology
H282P
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
ARHGAP15
Bos taurus
cattle - (species)
Published - Accepted by Curator
ASP1
Acetic acid production
Coding,
SNP
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Marullo P; Aigle M; Bely M ; et al. (2007)
Single QTL mapping and nucleotide-level resolution of a physiologic trait in wine Saccharomyces cere[...]
GP00000104
APS1
P35181
Physiology
Asp142His
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
ASP1
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
asparagine synthetase (AS)
Silk yield
Unknown,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Association Mapping
Xiang H; Liu X; Li M ; et al. (2018)
The evolutionary road from wild moth to domestic silkworm.
1 Additional References
GP00002404
AsnS
Q7KTW9
Physiology
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
asparagine synthetase (AS)
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Gene Loss,
Complex Change
N
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000106
GA20OX1
Q39110
Morphology
Whole gene deletion N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000107
GA20OX1
Q39110
Morphology
-2bp at +297 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000108
GA20OX1
Q39110
Morphology
-1bp "G" at +324 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000109
GA20OX1
Q39110
Morphology
-5bp "G" at +545 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000110
GA20OX1
Q39110
Morphology
-10bp "G" at +784 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000111
GA20OX1
Q39110
Morphology
-29bp at +426 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000112
GA20OX1
Q39110
Morphology
-444bp at +985 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Insertion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000113
GA20OX1
Q39110
Morphology
+1bp "G" at +256 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Insertion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000114
GA20OX1
Q39110
Morphology
+7bp "G" at +961 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Insertion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000115
GA20OX1
Q39110
Morphology
+1bp at +1270 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
Insertion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000116
GA20OX1
Q39110
Morphology
Transposon insertion at +1355 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
SNP
N
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000117
GA20OX1
Q39110
Morphology
W46* N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
SNP
N
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
1 Additional References
GP00000118
GA20OX1
Q39110
Morphology
W271* -G816A according to Fig.3 of Xu et al. 1995 N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
SNP
N
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000119
GA20OX1
Q39110
Morphology
E312* N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
2 Mutations:
Coding
SNP
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000120
GA20OX1
Q39110
Morphology
2 mutations
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Plant size (dwarfism)
2 Mutations:
Coding
SNP
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000121
GA20OX1
Q39110
Morphology
Morphology
2 mutations
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
2 Mutations:
Coding
SNP
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000122
GA20OX1
Q39110
Morphology
2 mutations
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
Coding,
SNP
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00000123
GA20OX1
Q39110
Morphology
Splice Site mutation G742A
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
AtGA20ox1 (=GA5=Sd1)
Plant size (dwarfism)
2 Mutations:
Coding
SNP
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Barboza L; Effgen S; Alonso-Blanco C ; et al. (2013)
Arabidopsis semidwarfs evolved from independent mutations in GA20ox1, ortholog to green revolution d[...]
GP00001685
GA20OX1
Q39110
Morphology
2 mutations
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
AtGA20ox1 (=GA5=Sd1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
B2
Coloration (bulb)
Cis-regulatory,
Insertion
N
Allium cepa
onion - (species) D
Domesticated
Linkage Mapping
Jo C; Kim S (2019)
Transposition of a non-autonomous DNA transposon in the gene coding for a bHLH transcription factor [...]
GP00002058
Morphology
577-bp insertion of a transposable element named AcWHITE in the 5′ upstream region of the white allele of B2. A 8-bp target site duplication (GTTATA AC) and a 7-bp terminal inverted repeat (CAAGGTT) were identified at both ends of this insertion - no SNP detected in the coding region N
Allium cepa
onion - (species)
Allium cepa
onion - (species) D
B2
Allium cepa
onion - (species)
Published - Accepted by Curator
B4GALNT2
Fertility (increased ovulation rate)
Cis-regulatory,
Unknown
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Drouilhet L; Mansanet C; Sarry J ; et al. (2013)
The highly prolific phenotype of Lacaune sheep is associated with an ectopic expression of the B4GAL[...]
GP00001979
B4galnt2
Q09199
Physiology
candidate region to 197kb ; putative mutation (g.36938224T>A) in intron 7or (g.37034573A>G) 96 kb away in an intergenic region
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
B4GALNT2
Ovis aries
sheep - (species)
Published - Accepted by Curator
B4GALT7
Body size (dwarfism)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Leegwater PA; Vos-Loohuis M; Ducro BJ ; et al. (2016)
Dwarfism with joint laxity in Friesian horses is associated with a splice site mutation in B4GALT7.
GP00002151
B4GALT7
Q9UBV7
Morphology
g.3,772,591C>T ; c.50G>A ; p.R17K ; last nucleotide of exon 1 and leads to a splicing deficiency of B4GALT7 transcripts ; All 29 dwarfs of which DNA was available were homozygous for the mutation . . . the 8 obligate carriers were heterozygous
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
B4GALT7
Equus caballus
horse - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
SNP
Glycine max
soybean - (species)
Domesticated
Linkage Mapping
Juwattanasomran R; Somta P; Chankaew S ; et al. (2011)
A SNP in GmBADH2 gene associates with fragrance in vegetable soybean variety "Kaori" and SNAP marker[...]
GP00000133
BADH2
Q84LK3
Physiology
1 amino-acid substitution in conserved enzymatic domain
Glycine max
soybean - (species)
Glycine max
soybean - (species)
BADH2
Glycine max
soybean - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Deletion
N
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Bradbury LM; Fitzgerald TL; Henry RJ ; et al. (2005)
The gene for fragrance in rice.
1 Additional References
GP00000134
BADH2
Q84LK3
Physiology
8bp deletion resulting in premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Shi Weiwei; Yang Yi; Chen Saihua ; et al. (2008
)
Discovery of a new fragrance allele and the development of functional markers for the breeding of fr[...]
1 Additional References
GP00001772
BADH2
Q84LK3
Physiology
7-bp deletion in exon 2 resulting in premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001773
BADH2
Q84LK3
Physiology
2-bp deletion in exon 1 resulting in premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Insertion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001774
BADH2
Q84LK3
Physiology
insertion of 1 bp (T) in exon 10 N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001775
BADH2
Q84LK3
Physiology
G>T substitution in exon 10 - need to check the sequence to check if this mutation is nonsense or nonsynonymous N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001776
BADH2
Q84LK3
Physiology
G>T substitution in exon 14 - need to check the sequence to check if this mutation is nonsense or nonsynonymous N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001777
BADH2
Q84LK3
Physiology
C>T substitution in exon 13 - need to check the sequence to check if this mutation is nonsense or nonsynonymous N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001778
BADH2
Q84LK3
Physiology
1-bp deletion in exon 10 - causes a frameshift N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Insertion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001779
BADH2
Q84LK3
Physiology
1-bp insertion (G) in exon 14 N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
BADH2
Fragrance
Coding,
Insertion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Kovach MJ; Calingacion MN; Fitzgerald MA ; et al. (2009)
The origin and evolution of fragrance in rice (Oryza sativa L.).
GP00001780
BADH2
Q84LK3
Physiology
3-bp insertion (TAT) in exon 13 - causes a frameshift N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
BADH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
Barren inflorescence2 (BIF2)
Plant architecture
Inflorescence architecture
Unknown,
Unknown
Zea mays
(species)
Domesticated
Linkage Mapping
Pressoir G; Brown PJ; Zhu W ; et al. (2009)
Natural variation in maize architecture is mediated by allelic differences at the PINOID co-ortholog[...]
1 Additional References
GP00000135
bif2
A6MW92
Morphology
Morphology
unknown
Zea mays
(species)
Zea mays
(species)
Barren inflorescence2 (BIF2)
Zea mays
(species)
Published - Accepted by Curator
BBS9 (+ BMPER)
Growth rate
Coding,
Deletion
N
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Association Mapping
Derks MFL; Lopes MS; Bosse M ; et al. (2018)
Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes[...]
GP00002341
Bbs9
Q811G0
Physiology
212kb deletion resulting in truncated BBS9 protein and recessive loss of neighbor gene expression BMPER N
Sus scrofa domesticus
domestic pig - (subspecies)
Sus scrofa domesticus
domestic pig - (subspecies) D
BBS9 (+ BMPER)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
BCMO1
Carotenoid content
2 Mutations:
Cis-regulatory
SNP
Gallus gallus
chicken - (species)
Domesticated
Linkage Mapping
Le Bihan-Duval E; Nadaf J; Berri C ; et al. (2011)
Detection of a Cis [corrected] eQTL controlling BCMO1 gene expression leads to the identification of[...]
GP00000137
BCO1
Q9HAY6
Morphology; Physiology
2 mutations
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
BCMO1
Gallus gallus
chicken - (species)
Published - Accepted by Curator
BCO2 = beta-carotene oxygenase 2
Carotenoid content (yellow serum)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Berry SD; Davis SR; Beattie EM ; et al. (2009)
Mutation in bovine beta-carotene oxygenase 2 affects milk color.
1 Additional References
GP00000138
BCO2
Q9BYV7
Physiology
c.306G>A ; p.W102* N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
BCO2 = beta-carotene oxygenase 2
Bos taurus
cattle - (species)
Published - Accepted by Curator
BCO2 = beta-carotene oxygenase 2
Carotenoid content (yellow fat)
Coding,
SNP
N
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Våge DI; Boman IA (2010)
A nonsense mutation in the beta-carotene oxygenase 2 (BCO2) gene is tightly associated with accumula[...]
1 Additional References
GP00000140
BCO2
Q9BYV7
Physiology
g.21947481C>T ; c.196C>T ; p.Q66* N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
BCO2 = beta-carotene oxygenase 2
Ovis aries
sheep - (species)
Published - Accepted by Curator
BCO2 = beta-carotene oxygenase 2
Carotenoid content (bill, legs)
Coding,
SNP
N
Serinus canaria
common canary - (species) D
Domesticated
Association Mapping
Gazda MA; Toomey MB; Araújo PM ; et al. (2020)
GENETIC BASIS OF DE NOVO APPEARANCE OF CAROTENOID ORNAMENTATION IN BARE-PARTS OF CANARIES.
GP00002039
BCO2
Q9BYV7
Morphology
point mutation at nucleotide position 837,806 that is predicted to be a nonsynonymous mutation in the exon 9 of the BCO2 gene. This variant results in the substitution of a histidine for an arginine at residue 413 of the protein (R413H) . In silico analysis suggests that the R413H could cause structural distortion of the protein and lead to a possible loss of activity. In vitro assays with the urucum BCO2 variant show that the enzyme activity is lost. N
Serinus canaria
common canary - (species)
Serinus canaria
common canary - (species) D
BCO2 = beta-carotene oxygenase 2
Serinus canaria
common canary - (species)
Published - Accepted by Curator
BCO2 = beta-carotene oxygenase 2
Carotenoid content (yellow fat)
Coding,
Deletion
N
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Strychalski J; Brym P; Czarnik U ; et al. (2015)
A novel AAT-deletion mutation in the coding sequence of the BCO2 gene in yellow-fat rabbits.
GP00002152
BCO2
Q9BYV7
Physiology
AAT-deletion mutation at Asp codon 248 of the BCO2 gene located at the beginning of exon 6 which results in the removal of an Asp N
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
BCO2 = beta-carotene oxygenase 2
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
beta-casein
Milk protein content (casein)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Gallinat JL; Qanbari S; Drögemüller C ; et al. (2013)
DNA-based identification of novel bovine casein gene variants.
GP00002025
CSN2
P02666
Physiology
g.87181619A>C c.245A>C p.H82P CAT>CCT
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
beta-casein
Bos taurus
cattle - (species)
Published - Accepted by Curator
beta-defensin 103 (CBD103)
Coloration (coat)
Coding,
Deletion
Canis lupus familiaris
dog - (subspecies) D
Canis latrans
coyote - (species) D
Canis lupus
gray wolf - (species) D
Domesticated
Linkage Mapping
Candille SI; Kaelin CB; Cattanach BM ; et al. (2007)
A -defensin mutation causes black coat color in domestic dogs.
2 Additional References
GP00000141
CBD103
Q30KV0
Morphology; Physiology
3bp in-frame deletion in exon 2 = deletion of Gly23
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Canis latrans
coyote - (species) D
Canis lupus
gray wolf - (species) D
beta-defensin 103 (CBD103)
Canis lupus familiaris
dog - (subspecies)
Canis latrans
coyote - (species)
Canis lupus
gray wolf - (species)
Published - Accepted by Curator
Bh4
Coloration (seed hull)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Zhu BF; Si L; Wang Z ; et al. (2011)
Genetic control of a transition from black to straw-white seed hull in rice domestication.
1 Additional References
GP00000143
Bh4
A0A0H3ZGK8
Morphology
22-bp deletion N
Oryza rufipogon
(species)
Oryza sativa
rice - (species) D
Bh4
Oryza sativa
rice - (species)
Published - Accepted by Curator
bHLH2
Coloration (flower; seed)
Coding,
Insertion
N
Ipomoea purpurea
common morning-glory - (species) D
Domesticated
Candidate Gene
Park KI; Ishikawa N; Morita Y ; et al. (2007)
A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthe[...]
GP00002078
BHLH2
Q9CAD0
Morphology
two copies of 3.9-kb Tip100 integrated into bHLH2 exon 7 and intron 2 N
Ipomoea purpurea
common morning-glory - (species)
Ipomoea purpurea
common morning-glory - (species) D
bHLH2
Ipomoea purpurea
common morning-glory - (species)
Published - Accepted by Curator
bHLH2
Coloration (flower; seed)
Coding,
Insertion
N
Ipomoea purpurea
common morning-glory - (species) D
Domesticated
Candidate Gene
Park KI; Ishikawa N; Morita Y ; et al. (2007)
A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthe[...]
GP00002085
BHLH2
Q9CAD0
Morphology
only one copy of Tip100 in exon 7 and no apparent footprint of Tip100 in intron 2 N
Ipomoea purpurea
common morning-glory - (species)
Ipomoea purpurea
common morning-glory - (species) D
bHLH2
Ipomoea purpurea
common morning-glory - (species)
Published - Accepted by Curator
bHLH2
Coloration (flower; seed)
Coding,
Insertion
N
Ipomoea purpurea
common morning-glory - (species) D
Domesticated
Candidate Gene
Park KI; Ishikawa N; Morita Y ; et al. (2007)
A bHLH regulatory gene in the common morning glory, Ipomoea purpurea, controls anthocyanin biosynthe[...]
GP00002086
BHLH2
Q9CAD0
Morphology
insertion of 838 bp IpMu1 in exon 2 N
Ipomoea purpurea
common morning-glory - (species)
Ipomoea purpurea
common morning-glory - (species) D
bHLH2
Ipomoea purpurea
common morning-glory - (species)
Published - Accepted by Curator
bHLH2
Coloration (flowers; seeds)
Coding,
Insertion
N
Ipomoea tricolor
(species) D
Domesticated
Candidate Gene
Park KI; Choi JD; Hoshino A ; et al. (2004)
An intragenic tandem duplication in a transcriptional regulatory gene for anthocyanin biosynthesis c[...]
GP00002091
BHLH2
Q9CAD0
Morphology
intragenic tandem duplication of 3.3 kbp of the bHLH2 gene. Each of the tandem repeats is flanked by a 3-bp sequence AAT; indicating that the 3-bp microhomology is used to generate the tandem duplication. The transcripts in the pale-blue flower buds of the mutant contain an internal 583-bp tandem duplication that results in the production of a truncated polypeptide lacking the bHLH domain. The mRNA accumulation of most of the structural genes encoding enzymes for anthocyanin biosynthesis in the flower buds of the mutant was significantly reduced. The transcripts identical to the wild-type mRNAs for the transcriptional activator were present abundantly in blue spots of the variegated flowers whereas the transcripts containing the 583-bp tandem duplication were predominant in the pale-blue background of the same flowers. The flower and seed variegations studied here are likely to be caused by somatic homologous recombination between an intragenic tandem duplication in the gene encoding a bHLH transcriptional activator for anthocyanin biosynthesis. N
Ipomoea tricolor
(species)
Ipomoea tricolor
(species) D
bHLH2
Ipomoea tricolor
(species)
Published - Accepted by Curator
bHLH2
Coloration (flowers)
Coding,
Insertion
N
Petunia axillaris
(species) D
Domesticated
Candidate Gene
Spelt C; Quattrocchio F; Mol J ; et al. (2002)
ANTHOCYANIN1 of petunia controls pigment synthesis, vacuolar pH, and seed coat development by geneti[...]
GP00002092
BHLH2
Q9CAD0
Morphology
insertion of a dTph1 transposon in the AN1 gene N
Petunia axillaris
(species)
Petunia axillaris
(species) D
bHLH2
Petunia axillaris
(species)
Published - Accepted by Curator
Bm-iAANAT
Coloration (larva)
Coding,
Deletion
N
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Zhan S; Guo Q; Li M ; et al. (2010)
Disruption of an N-acetyltransferase gene in the silkworm reveals a novel role in pigmentation.
1 Additional References
GP00000145
Aanat
D6MKR2
Morphology
126-bp deletion overlapping with end of exon 4 and resulting in misplicing. Linkage analysis and genomic studies have shown that Bombyx arylalkamine-N-acetyl transferase, the homologous gene (Dat) that converts dopamine into N-acetyl dopamine, encodes a precursor of N-acetyl dopamine, sclerotin in Drosophila and it is the gene responsible for mln. N
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Bm-iAANAT
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
BMP receptor IB (BMPRIB)
Fertility (increased ovulation rate)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Mulsant P; Lecerf F; Fabre S ; et al. (2001)
Mutation in bone morphogenetic protein receptor-IB is associated with increased ovulation rate in Bo[...]
GP00000146
BMPR-IB
Q9BDI4
Physiology
g.29382188A>G c.914A>G p.Q305R
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
BMP receptor IB (BMPRIB)
Ovis aries
sheep - (species)
Published - Accepted by Curator
BMP15
Fertility (increased ovulation rate)
Coding,
SNP
N
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Galloway SM; McNatty KP; Cambridge LM ; et al. (2000)
Mutations in an oocyte-derived growth factor gene (BMP15) cause increased ovulation rate and inferti[...]
GP00000147
Bmp15
Q9Z0L4
Physiology
c.67C>T p.Q23* N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
BMP15
Ovis aries
sheep - (species)
Published - Accepted by Curator
BMP15
Fertility (increased ovulation rate)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Galloway SM; McNatty KP; Cambridge LM ; et al. (2000)
Mutations in an oocyte-derived growth factor gene (BMP15) cause increased ovulation rate and inferti[...]
GP00000148
Bmp15
Q9Z0L4
Physiology
A distinct single T>A transition occurs in FecXI carriers at nucleotide position 92 of the mature peptide . . . The mutation substitutes valine (V) with aspartic acid (D) at residue 31 (residue 299 of unprocessed protein) . . . The FecXI mutation is a non-conservative change in a highly conserved region of the protein
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
BMP15
Ovis aries
sheep - (species)
Published - Accepted by Curator
BMP15
Fertility (increased ovulation rate)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Association Mapping
Demars J; Fabre S; Sarry J ; et al. (2013)
Genome-wide association studies identify two novel BMP15 mutations responsible for an atypical hyper[...]
GP00000149
Bmp15
Q9Z0L4
Physiology
c.950C>T p.T317I
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
BMP15
Ovis aries
sheep - (species)
Published - Accepted by Curator
BMP15
Fertility (increased ovulation rate)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Association Mapping
Demars J; Fabre S; Sarry J ; et al. (2013)
Genome-wide association studies identify two novel BMP15 mutations responsible for an atypical hyper[...]
GP00000150
Bmp15
Q9Z0L4
Physiology
c.1009A>C p.N337H
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
BMP15
Ovis aries
sheep - (species)
Published - Accepted by Curator
BMP15
Fertility (increased ovulation rate)
Coding,
SNP
N
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Hanrahan JP; Gregan SM; Mulsant P ; et al. (2004)
Mutations in the genes for oocyte-derived growth factors GDF9 and BMP15 are associated with both inc[...]
GP00002155
Bmp15
Q9Z0L4
Physiology
c.718C>T ; p.Q239* N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
BMP15
Ovis aries
sheep - (species)
Published - Accepted by Curator
BMP15
Fertility (increased ovulation rate)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Galloway SM; McNatty KP; Cambridge LM ; et al. (2000)
Mutations in an oocyte-derived growth factor gene (BMP15) cause increased ovulation rate and inferti[...]
GP00002156
Bmp15
Q9Z0L4
Physiology
c.G>A p.C321Y missense nonconservative substitution ; in vitro studies showed that the C53Y mutation was responsible for the impairment of the maturation process of the BMP15 protein resulting in a defective secretion of both the precursor and mature peptide
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
BMP15
Ovis aries
sheep - (species)
Published - Accepted by Curator
BMP15
Fertility (increased ovulation rate)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Hanrahan JP; Gregan SM; Mulsant P ; et al. (2004)
Mutations in the genes for oocyte-derived growth factors GDF9 and BMP15 are associated with both inc[...]
GP00002157
Bmp15
Q9Z0L4
Physiology
c.1100G>T p.S367I
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
BMP15
Ovis aries
sheep - (species)
Published - Accepted by Curator
BMP15
Fertility (increased ovulation rate)
Coding,
Deletion
N
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Martinez-Royo A; Jurado JJ; Smulders JP ; et al. (2008)
A deletion in the bone morphogenetic protein 15 gene causes sterility and increased prolificacy in R[...]
1 Additional References
GP00002158
Bmp15
Q9Z0L4
Physiology
c.525_541del17 p.Pro45Asnfs*54 N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
BMP15
Ovis aries
sheep - (species)
Published - Accepted by Curator
BMP15
Fertility (increased ovulation rate)
Coding,
Insertion
N
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Lassoued N; Benkhlil Z; Woloszyn F ; et al. (2017)
FecX a Novel BMP15 mutation responsible for prolificacy and female sterility in Tunisian Barbarine [...]
GP00002159
Bmp15
Q9Z0L4
Physiology
C insertion (c.310insC) in the ovine BMP15 cDNA leading to a frame shift at protein position 101 N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
BMP15
Ovis aries
sheep - (species)
Published - Accepted by Curator
BMP15
Fertility (increased ovulation rate)
Cis-regulatory,
SNP
Ovis aries
sheep - (species) D
Domesticated
Association Mapping
Demars J; Fabre S; Sarry J ; et al. (2013)
Genome-wide association studies identify two novel BMP15 mutations responsible for an atypical hyper[...]
GP00002329
Bmp15
Q9Z0L4
Physiology
T>A SPN upstream of the BMP15 gene associated with the prolificacy variability (P = 1.93E-11). Effect of +0.20 lamb per lambing at the heterozygous state.
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
BMP15
Ovis aries
sheep - (species)
Published - Accepted by Curator
BMP2
Fertility (egg production)
Bird head morphology (male comb)
Cis-regulatory,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Linkage Mapping
Johnsson M; Gustafson I; Rubin CJ ; et al. (2012)
A sexual ornament in chickens is affected by pleiotropic alleles at HAO1 and BMP2, selected during d[...]
1 Additional References
GP00000151
BMP2
Q90751
Physiology
Morphology
unknown; but intergenic QTL peak with decomposed effects on expression of BMP2 and HAO1
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
BMP2
Gallus gallus
chicken - (species)
Published - Accepted by Curator
BMP3 or PRKG2
Cranio-facial morphology
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Schoenebeck JJ; Hutchinson SA; Byers A ; et al. (2012)
Variation of BMP3 contributes to dog breed skull diversity.
GP00000152
Bmp3
Q8BHE5
Morphology
F452L in BMP3 ; this missense mutation is in a conserved position and correlates well with small breeds. However; the functional data (zebrafish BMP3 morpholino knockdown) proposed in this article is inconsistent with the mice BMP3 null-mutation
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
BMP3 or PRKG2
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
BOLTING TIME CONTROL 1 (BvBTC1)
Flowering time
Cis-regulatory,
Unknown
Beta vulgaris
(species)
Domesticated
Linkage Mapping
Pin PA; Zhang W; Vogt SH ; et al. (2012)
The role of a pseudo-response regulator gene in life cycle adaptation and domestication of beet.
GP00000155
BTC1
I3NN18
Physiology
unknown
Beta vulgaris
(species)
Beta vulgaris
(species)
BOLTING TIME CONTROL 1 (BvBTC1)
Beta vulgaris
(species)
Published - Accepted by Curator
brittle endosperm2 (Bt2) = endosperm ADP-glucose pyrophosphorylase small subunit
Sweet and brittle seed
Unknown,
Unknown
Zea mays
(species)
Domesticated
Linkage Mapping
Preiss J; Danner S; Summers PS ; et al. (1990)
Molecular Characterization of the Brittle-2 Gene Effect on Maize Endosperm ADPglucose Pyrophosphoryl[...]
GP00000158
bt2
Q84J79
Physiology
Not identified
Zea mays
(species)
Zea mays
(species)
brittle endosperm2 (Bt2) = endosperm ADP-glucose pyrophosphorylase small subunit
Zea mays
(species)
Published - Accepted by Curator
Brix9-2-5/LIN5 invertase
Fruit sugar content
Unknown,
Unknown
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Fridman E; Carrari F; Liu YS ; et al. (2004)
Zooming in on a quantitative trait for tomato yield using interspecific introgressions.
GP00000159
LIN5
P93199
Physiology
Not identified
Solanum pennellii
(species)
Solanum lycopersicum
tomato - (species) D
Brix9-2-5/LIN5 invertase
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
BTN1A1
Pathogen resistance (virus)
Coding,
SNP
N
Gallus gallus
chicken - (species)
Domesticated
Linkage Mapping
Elleder D; Stepanets V; Melder DC ; et al. (2005)
The receptor for the subgroup C avian sarcoma and leukosis viruses, Tvc, is related to mammalian but[...]
GP00002160
BTN1A1
Q13410
Physiology
g.808011C>A c.165C>A p.C55* N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
BTN1A1
Gallus gallus
chicken - (species)
Published - Accepted by Curator
btr1
Seed shattering (grain dispersal ; retention)
Coding,
Deletion
N
Hordeum vulgare subsp. vulgare
domesticated barley - (subspecies) D
Domesticated
Linkage Mapping
Pourkheirandish M; Hensel G; Kilian B ; et al. (2015)
Evolution of the Grain Dispersal System in Barley.
GP00001445
BTR1
A0A0K1RJT0
Physiology
1bp deletion at position 202 inducing a frameshift N
Hordeum vulgare
(species)
Hordeum vulgare subsp. vulgare
domesticated barley - (subspecies) D
btr1
Hordeum vulgare subsp. vulgare
domesticated barley - (subspecies)
Published - Accepted by Curator
btr2
Seed shattering (grain dispersal ; retention)
Coding,
Deletion
N
Hordeum vulgare subsp. vulgare
domesticated barley - (subspecies) D
Domesticated
Linkage Mapping
Pourkheirandish M; Hensel G; Kilian B ; et al. (2015)
Evolution of the Grain Dispersal System in Barley.
GP00001446
BTR2
A0A0K1RKV9
Physiology
11bp deletion at position 254-264 creating a frameshift N
Hordeum vulgare
(species)
Hordeum vulgare subsp. vulgare
domesticated barley - (subspecies) D
btr2
Hordeum vulgare subsp. vulgare
domesticated barley - (subspecies)
Published - Accepted by Curator
BUL2
Telomere length
Aging
Coding,
SNP
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Kwan EX; Foss E; Kruglyak L ; et al. (2011)
Natural polymorphism in BUL2 links cellular amino acid availability with chronological aging and tel[...]
GP00000166
BUL2
Q03758
Physiology
Physiology
Leu883Phe
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
BUL2
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
c1
Coloration (seed)
Cis-regulatory,
Insertion
Zea mays
(species) D
Domesticated
Linkage Mapping
Hattori T; Vasil V; Rosenkrans L ; et al. (1992)
The Viviparous-1 gene and abscisic acid activate the C1 regulatory gene for anthocyanin biosynthesis[...]
1 Additional References
GP00000167
C1
P10290
Morphology
5bp insertion in the proximal promoter that creates a new binding site for VP1; a transcription factor that regulates kernel maturation; so that the pigment pathway is turned on while the kernel matures; giving blue kernels
Zea mays
(species)
Zea mays
(species) D
c1
Zea mays
(species)
Published - Accepted by Curator
Callipyge (CLPG1)
Muscular mass (double-muscling ; paternal effect)
Cis-regulatory,
SNP
Ovis aries
sheep - (species)
Domesticated
Linkage Mapping
Takeda H; Caiment F; Smit M ; et al. (2006)
The callipyge mutation enhances bidirectional long-range DLK1-GTL2 intergenic transcription in cis.
5 Additional References
GP00000168
DIO3
Q6DN07
Morphology; Physiology
1bp change in the regulatory region of the DLK1-GTL2 imprinted gene cluster
Ovis aries
sheep - (species)
Ovis aries
sheep - (species)
Callipyge (CLPG1)
Ovis aries
sheep - (species)
Published - Accepted by Curator
cardinal
Coloration (eyes)
Coding,
Insertion
N
Tribolium castaneum
red flour beetle - (species) D
Domesticated
Candidate Gene
Shirai Y; Daimon T (2020)
Mutations in cardinal are responsible for the red-1 and peach eye color mutants of the red flour bee[...]
GP00002665
cd
Q9VCW2
Morphology
A fragment of a transposable element (about 5 kb - 99% identical in amino acids to a putative retrotransposon (XP_015838217)) is inserted into exon 6. This insertion introduced a premature stop codon just after the insertion site. Amino acid residues near the C-terminal end of the haem peroxidase domain are thus disrupted. N
Tribolium castaneum
red flour beetle - (species)
Tribolium castaneum
red flour beetle - (species) D
cardinal
Tribolium castaneum
red flour beetle - (species)
Published - Accepted by Curator
cardinal
Coloration (eyes)
Coding,
Deletion
N
Tribolium castaneum
red flour beetle - (species) D
Domesticated
Candidate Gene
Shirai Y; Daimon T (2020)
Mutations in cardinal are responsible for the red-1 and peach eye color mutants of the red flour bee[...]
GP00002666
cd
Q9VCW2
Morphology
1-bp deletion in exon 6 that causes a frameshift mutation. Amino acid residues near the C-terminal end of the haem peroxidase domain are thus disrupted. N
Tribolium castaneum
red flour beetle - (species)
Tribolium castaneum
red flour beetle - (species) D
cardinal
Tribolium castaneum
red flour beetle - (species)
Published - Accepted by Curator
cardinal
Coloration (eyes)
Coding,
SNP
N
Bombyx mori
domestic silkworm - (species) D
Domesticated
Candidate Gene
Osanai-Futahashi M; Tatematsu KI; Futahashi R ; et al. (2016)
Positional cloning of a Bombyx pink-eyed white egg locus reveals the major role of cardinal in ommoc[...]
GP00002667
cd
Q9VCW2
Morphology
Missense mutation in a conserved motif in exon 9. The tryptophan residue which is converted to arginine in the two pe strains is widely conserved in holometabolous insects. N
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
cardinal
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
Carotenoid-binding protein (CBP)
Coloration (silk)
Gene Amplification,
Complex Change
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Sakudoh T; Nakashima T; Kuroki Y ; et al. (2011)
Diversity in copy number and structure of a silkworm morphogenetic gene as a result of domestication[...]
1 Additional References
GP00000169
Q1HE01
Morphology
Copy Number Variation (up to 20 copies in B. mori ; only one in the wild form; B. mandarina)
Bombyx mandarina
wild silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Carotenoid-binding protein (CBP)
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
CAST
Meat tenderness
Cis-regulatory,
Unknown
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Nonneman D; Lindholm-Perry AK; Shackelford SD ; et al. (2011)
Predictive markers in calpastatin for tenderness in commercial pig populations.
GP00000170
CAST
P20810
Physiology
4 candidate SNPs in putative enhancers with nuclear factor-binding properties
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
CAST
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Cauliflower (BoCAL)
Inflorescence morphology
Coding,
SNP
N
Brassica oleracea var. botrytis
(varietas) D
Domesticated
Candidate Gene
Kempin SA; Savidge B; Yanofsky MF (1995)
Molecular basis of the cauliflower phenotype in Arabidopsis.
1 Additional References
GP00000173
CAL
Q39081
Morphology
GAG>TAG; E151*; protein truncated after only 150 of the 255 amino acids of the wild-type protein N
Brassica oleracea
wild cabbage - (species)
Brassica oleracea var. botrytis
(varietas) D
Cauliflower (BoCAL)
Brassica oleracea var. botrytis
(varietas)
Published - Accepted by Curator
CBF12
Temperature tolerance (cold)
Coding,
Unknown
Triticum monococcum
(species)
Domesticated
Linkage Mapping
Knox AK; Li C; Vágújfalvi A ; et al. (2008)
Identification of candidate CBF genes for the frost tolerance locus Fr-Am2 in Triticum monococcum.
GP00000175
B1NSN2
Physiology
possibly 5a.a. deletion in DNA binding domain
Triticum monococcum
(species)
Triticum monococcum
(species)
CBF12
Triticum monococcum
(species)
Published - Accepted by Curator
CBF2-CBF4; CBF13
Temperature tolerance (cold)
Gene Amplification,
Complex Change
Hordeum vulgare
(species)
Domesticated
Candidate Gene
Knox AK; Dhillon T; Cheng H ; et al. (2010)
CBF gene copy number variation at Frost Resistance-2 is associated with levels of freezing tolerance[...]
GP00000176
B1NSN2
Physiology
tandem duplication of CBF2-CBF4 region and/or pseudogenisation of CBF13
Hordeum vulgare
(species)
Hordeum vulgare
(species)
CBF2-CBF4; CBF13
Hordeum vulgare
(species)
Published - Accepted by Curator
CDKN2A
Coloration (feathers ; sex-linked dilution)
2 Mutations:
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Schwochow Thalmann D; Ring H; Sundström E ; et al. (2017)
The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes [...]
1 Additional References
GP00000178
CDKN2A
P42771
Morphology
2 mutations
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
CDKN2A
Gallus gallus
chicken - (species)
Published - Accepted by Curator
CDKN2A
Coloration (feathers ; sex-linked barring)
2 Mutations:
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Schwochow Thalmann D; Ring H; Sundström E ; et al. (2017)
The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes [...]
1 Additional References
GP00002162
CDKN2A
P42771
Morphology
2 mutations
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
CDKN2A
Gallus gallus
chicken - (species)
Published - Accepted by Curator
CENTRORADIALIS (HvCEN)
Flowering time
Seasonal growth
Coding,
SNP
Hordeum vulgare
(species)
Domesticated
Linkage Mapping
Comadran J; Kilian B; Russell J ; et al. (2012)
Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and [...]
GP00000179
CEN
Q9ZNV5
Physiology
Physiology
P135A
Hordeum vulgare
(species)
Hordeum vulgare
(species)
CENTRORADIALIS (HvCEN)
Hordeum vulgare
(species)
Published - Accepted by Curator
CEP55
Recombination rate (female)
Unknown,
Unknown
Bos taurus
cattle - (species)
Domesticated
Association Mapping
Ma L; O'Connell JR; VanRaden PM ; et al. (2015)
Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.
GP00001667
CEP55
E1B8M0
Physiology
Associated SNP located near the gene
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
CEP55
Bos taurus
cattle - (species)
Published - Accepted by Curator
Cf-2.1 and Cf-2.2
Pathogen resistance (leaf mold fungus ; root parasitic nematode)
Gene Loss,
Deletion
N
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Dixon MS; Jones DA; Keddie JS ; et al. (1996)
The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat[...]
2 Additional References
GP00000180
Q41398
Physiology
loss of the two genes Cf-2.1 and Cf-2.2 (see Dixon et al. 1998) in cultivated tomato - resistance re-acquired from related species N
Solanum pimpinellifolium
(species)
Solanum lycopersicum
tomato - (species) D
Cf-2.1 and Cf-2.2
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
Cf-4/9
Pathogen resistance
Gene Loss,
Complex Change
Solanum lycopersicum
tomato - (species)
Domesticated
Linkage Mapping
Parniske M; Hammond-Kosack KE; Golstein C ; et al. (1997)
Novel disease resistance specificities result from sequence exchange between tandemly repeated genes[...]
GP00000181
Cf-4A
Q7DLS4
Physiology
partial loss of two gene coding regions located in tandem; resulting in a chimeric gene
Solanum pimpinellifolium
(species)
Solanum lycopersicum
tomato - (species)
Cf-4/9
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
Chit beta-GlcNAcase
Silk fineness
Cis-regulatory,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Association Mapping
Tong X; Han MJ; Lu K ; et al. (2022)
High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecologic[...]
GP00002401
P49010
Physiology
BmChit β-GlcNAcase gene is expressed at a significantly higher level in fine silk strains (Suxiu, Chunfeng) compared to coarse silk strains. CRISPR-cas9 mediated knockout of the BmChit β-GlcNAcase gene produced coarser silk.
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Chit beta-GlcNAcase
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
chordin
Fin morphology (skeleton; dorsal fin; caudal fin; tail; paired fin)
Coding,
SNP
N
Carassius auratus
goldfish - (species) D
Domesticated
Candidate Gene
Abe G; Lee SH; Chang M ; et al. (2014)
The origin of the bifurcated axial skeletal system in the twin-tail goldfish.
1 Additional References
GP00002346
chdA
W8VTE1
Morphology
stop codon in codon 127. GAG (E) -> TAG (STOP). Predicted to result in a truncated protein lacking the second to fourth CR domains. N
Carassius auratus
goldfish - (species)
Carassius auratus
goldfish - (species) D
chordin
Carassius auratus
goldfish - (species)
Published - Accepted by Curator
CINNAMOYL CO-A REDUCTASE 1
Fiber content
Coding,
Unknown
N
Brassica napus
rape - (species)
Domesticated
Linkage Mapping
Liu L; Stein A; Wittkop B ; et al. (2012)
A knockout mutation in the lignin biosynthesis gene CCR1 explains a major QTL for acid detergent lig[...]
GP00000186
CCR1
Q9S9N9
Physiology
Frameshift mutation in exon1 N
Brassica napus
rape - (species)
Brassica napus
rape - (species)
CINNAMOYL CO-A REDUCTASE 1
Brassica napus
rape - (species)
Published - Accepted by Curator
CIS1
Xenobiotic resistance (citrinin)
Cis-regulatory,
Unknown
Saccharomyces paradoxus
(species) D
Domesticated
Association Mapping
Naranjo S; Smith JD; Artieri CG ; et al. (2015)
Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation.
GP00001313
ATG31
Q12421
Physiology
mutations within 1kb in promotor region
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces paradoxus
(species) D
CIS1
Saccharomyces paradoxus
(species)
Published - Accepted by Curator
Clock
Circadian rhythm
Unknown,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Association Mapping
Xiang H; Liu X; Li M ; et al. (2018)
The evolutionary road from wild moth to domestic silkworm.
1 Additional References
GP00002409
Clk
O61735
Physiology
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Clock
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
CLV3
Fruit size
Cis-regulatory,
Inversion
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Xu C; Liberatore KL; MacAlister CA ; et al. (2015)
A cascade of arabinosyltransferases controls shoot meristem size in tomato.
GP00001565
CLV3
Q9XF04
Morphology
A 294 kb inversion with a breakpoint 1 kb upstream of CLV3
Solanum pimpinellifolium
(species)
Solanum lycopersicum
tomato - (species) D
CLV3
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
cly1
Pollen shedding (Cleistogamy; lodicule size)
Cis-regulatory,
SNP
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Nair SK; Wang N; Turuspekov Y ; et al. (2010)
Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage[...]
1 Additional References
GP00001314
AP2
P47927
Morphology
A>G @position 3084; in a miRNA targeting site.
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
cly1
Hordeum vulgare
(species)
Published - Accepted by Curator
cly1
Pollen shedding (Cleistogamy; lodicule size)
Cis-regulatory,
SNP
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Nair SK; Wang N; Turuspekov Y ; et al. (2010)
Cleistogamous flowering in barley arises from the suppression of microRNA-guided HvAP2 mRNA cleavage[...]
1 Additional References
GP00001315
AP2
P47927
Morphology
A>C @position 3090; in a miRNA targeting site.
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
cly1
Hordeum vulgare
(species)
Published - Accepted by Curator
cly1
Pollen shedding (Cleistogamy; lodicule size)
Cis-regulatory,
Epigenetic Change
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Wang N; Ning S; Wu J ; et al. (2015)
An epiallele at cly1 affects the expression of floret closing (cleistogamy) in barley.
GP00001316
AP2
P47927
Morphology
T>C @position -245; creating differential methylation
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
cly1
Hordeum vulgare
(species)
Published - Accepted by Curator
CmACS-7
Flower sex determination (male organs)
Coding,
SNP
Cucumis melo
muskmelon - (species)
Domesticated
Linkage Mapping
Boualem A; Fergany M; Fernandez R ; et al. (2008)
A conserved mutation in an ethylene biosynthesis enzyme leads to andromonoecy in melons.
GP00000187
ACS7
Q9STR4
Physiology
A57V
Cucumis melo
muskmelon - (species)
Cucumis melo
muskmelon - (species)
CmACS-7
Cucumis melo
muskmelon - (species)
Published - Accepted by Curator
CmWIP1
Flower sex determination (female vs. hermaphrodite)
Cis-regulatory,
Insertion
Cucumis melo
muskmelon - (species) D
Domesticated
Linkage Mapping
Martin A; Troadec C; Boualem A ; et al. (2009)
A transposon-induced epigenetic change leads to sex determination in melon.
GP00000188
WIP1
Q8GXA4
Physiology
Promoter insertion of a Transcription Factor Binding Site allowing propagation of heritable methylation
Cucumis melo
muskmelon - (species)
Cucumis melo
muskmelon - (species) D
CmWIP1
Cucumis melo
muskmelon - (species)
Published - Accepted by Curator
CNL9 (=Sr35)
Pathogen resistance
Coding,
Complex Change
Triticum monococcum
(species)
Domesticated
Linkage Mapping
Saintenac C; Zhang W; Salcedo A ; et al. (2013)
Identification of wheat gene Sr35 that confers resistance to Ug99 stem rust race group.
GP00000189
Sr35
S5ABD6
Physiology
Coding variation in the LRR domain - a spontaneous gene conversion between CNL4 and CNL9 is the most parsimonious explanation for the three linked mutations in CNL9
Triticum monococcum
(species)
Triticum monococcum
(species)
CNL9 (=Sr35)
Triticum monococcum
(species)
Published - Accepted by Curator
coatomer protein complex subunit alpha (COPA)
Coloration (coat)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Dorshorst B; Henegar C; Liao X ; et al. (2015)
Dominant Red Coat Color in Holstein Cattle Is Associated with a Missense Mutation in the Coatomer Pr[...]
GP00001329
COPA
P53621
Morphology
c.C>T p.Arg160Cys
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
coatomer protein complex subunit alpha (COPA)
Bos taurus
cattle - (species)
Published - Accepted by Curator
colored plant 1
Coloration (seed)
Cis-regulatory,
Unknown
Zea mays
(species)
Domesticated
Linkage Mapping
Radicella JP; Brown D; Tolar LA ; et al. (1992)
Allelic diversity of the maize B regulatory gene: different leader and promoter sequences of two B a[...]
GP00000190
b1
W5S3Q3
Morphology
Not identified
Zea mays
(species)
Zea mays
(species)
colored plant 1
Zea mays
(species)
Published - Accepted by Curator
cortex
Coloration (wing)
Cis-regulatory,
Deletion
Heliconius melpomene
postman butterfly - (species) D
Domesticated
Association Mapping
Hanly JJ; Livraghi L; Heryanto C ; et al. (2022)
A large deletion at the cortex locus eliminates butterfly wing patterning.
GP00001805
cort
Q960N3
Morphology
78-kb deletion in the 5′ region of the cortex gene that includes a facultative 5′UTR exon detected in larval wing disk transcriptomes. Phenotypic effect confirmed by CRISPR mutagenesis of this exon. The ivory deletion causes the loss of 1 of 2 promoters.
Heliconius melpomene
postman butterfly - (species)
Heliconius melpomene
postman butterfly - (species) D
cortex
Heliconius melpomene
postman butterfly - (species)
Published - Accepted by Curator
cortex
Coloration (wing ; body)
Unknown,
Unknown
Bombyx mori
domestic silkworm - (species)
Domesticated
Linkage Mapping
Ito K; Katsuma S; Kuwazaki S ; et al. (2016)
Mapping and recombination analysis of two moth colour mutations, Black moth and Wild wing spot, in t[...]
GP00002417
cort
Q960N3
Morphology
Mapping to a 2-Mb-long region which contains the cortex gene.
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species)
cortex
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
cortex
Coloration (wing)
Unknown,
Unknown
Bombyx mori
domestic silkworm - (species)
Domesticated
Linkage Mapping
Ito K; Katsuma S; Kuwazaki S ; et al. (2016)
Mapping and recombination analysis of two moth colour mutations, Black moth and Wild wing spot, in t[...]
GP00002418
cort
Q960N3
Morphology
Mapping to a 100-kb-long region which contains the cortex gene.
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species)
cortex
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
CPLX1
Recombination rate
Unknown,
Unknown
Bos taurus
cattle - (species)
Domesticated
Association Mapping
Ma L; O'Connell JR; VanRaden PM ; et al. (2015)
Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.
GP00001659
CPLX1
Q0IIL7
Physiology
On chromosome 6. Associated SNP in the intron of the gene
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
CPLX1
Bos taurus
cattle - (species)
Published - Accepted by Curator
Cryptochrome 2 (CRY2)
Circadian rhythm
Unknown,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Association Mapping
Xiang H; Liu X; Li M ; et al. (2018)
The evolutionary road from wild moth to domestic silkworm.
1 Additional References
GP00002408
cry
O77059
Physiology
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Cryptochrome 2 (CRY2)
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
CS
Plant secondary metabolite (pungency)
Cis-regulatory,
Deletion
N
Capsicum annuum
(species) D
Domesticated
Candidate Gene
Kim S; Park M; Yeom SI ; et al. (2014)
Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum speci[...]
1 Additional References
GP00001447
csy1
Q09UW1
Physiology
Large 2.5 kb deletion spanning 1.8 kb of the putative promoter and 0.7 kb of the first exon was observed in the C. annuum Bellpeppers N
Capsicum frutescens
(species)
Capsicum annuum
(species) D
CS
Capsicum annuum
(species)
Published - Accepted by Curator
CYP19A1
Coloration (feathers)
Cis-regulatory,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Candidate Gene
Li J; Davis BW; Jern P ; et al. (2019)
Characterization of the endogenous retrovirus insertion in CYP19A1 associated with henny feathering [...]
GP00002050
CYP19A1
P11511
Morphology
7524 bp insertion at the 5'end of CYP19A1 of an intact endogenous retrovirus (99% sequence identity to the avian leukosis virus ev-1 and ev-21 strains suggesting a recent integration) - The ERV 3'LTR contains a powerful transcriptional enhancer and core promoter with TATA box.
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
CYP19A1
Gallus gallus
chicken - (species)
Published - Accepted by Curator
CYP2J19
Coloration (red vs yellow beak)
Gene Loss,
Deletion
N
Taeniopygia guttata
zebra finch - (species) D
Domesticated
Linkage Mapping
Mundy NI; Stapley J; Bennison C ; et al. (2016)
Red Carotenoid Coloration in the Zebra Finch Is Controlled by a Cytochrome P450 Gene Cluster.
GP00000202
CYP2J2
P51589
Morphology
13kb deletion including complete loss of the CYP2J19A copy and cis-regulatory effects on CYP2J19B N
Taeniopygia guttata
zebra finch - (species)
Taeniopygia guttata
zebra finch - (species) D
CYP2J19
Taeniopygia guttata
zebra finch - (species)
Published - Accepted by Curator
CYP76AD1
Coloration
Coding,
Insertion
N
Beta vulgaris
(species) D
Domesticated
Linkage Mapping
Hatlestad GJ; Sunnadeniya RM; Akhavan NA ; et al. (2012)
The beet R locus encodes a new cytochrome P450 required for red betalain production.
GP00000210
CYP76AD1
I3PFJ5
Morphology
5bp insertion resulting in frameshift N
Beta vulgaris
(species)
Beta vulgaris
(species) D
CYP76AD1
Beta vulgaris
(species)
Published - Accepted by Curator
DCAF17
Hair Length
Unknown,
Unknown
Sus scrofa
pig - (species) D
Domesticated
Association Mapping
Ai H; Fang X; Yang B ; et al. (2015)
Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequen[...]
GP00001570
DCAF17
I3LQF0
Physiology
Sus scrofa
pig - (species)
Sus scrofa
pig - (species) D
DCAF17
Sus scrofa
pig - (species)
Published - Accepted by Curator
DCAR-032551
Carotenoid content
Coding,
Insertion
N
Daucus carota
carrot - (species) D
Domesticated
Linkage Mapping
Iorizzo M; Ellison S; Senalik D ; et al. (2016)
A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid[...]
GP00001568
DCAR_032551
A0A162A3G8
Morphology
A 212-nt insertion in exon 2 that creates a frameshift mutation N
Daucus carota
carrot - (species)
Daucus carota
carrot - (species) D
DCAR-032551
Daucus carota
carrot - (species)
Published - Accepted by Curator
DEEPER ROOTING 1
Drought tolerance
Root growth
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Uga Y; Sugimoto K; Ogawa S ; et al. (2013)
Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought condition[...]
GP00000215
Dro1
Q69P88
Physiology
Morphology
1bp deletion within exon 4 N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
DEEPER ROOTING 1
Oryza sativa
rice - (species)
Published - Accepted by Curator
DEFICIENS
Fruit shape
Cis-regulatory,
Epigenetic Change
Elaeis guineensis
African oil palm - (species) D
Domesticated
Association Mapping
Ong-Abdullah M; Ordway JM; Jiang N ; et al. (2015)
Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm.
GP00002100
AP3
P35632
Morphology
hypomethylation of the 3.2 kb oil palm Karma transposable element located within an intron of the DEFICIENS gene - this results in unmasking of a cryptic splice acceptor site and a premature termination signal and causes the mantled fruit phenotype- epigenetic derepression of a TE associated with a deleterious phenotype
Elaeis guineensis
African oil palm - (species)
Elaeis guineensis
African oil palm - (species) D
DEFICIENS
Elaeis guineensis
African oil palm - (species)
Published - Accepted by Curator
DEP1
Grain yield
Coding,
Indel
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Huang X; Qian Q; Liu Z ; et al. (2009)
Natural variation at the DEP1 locus enhances grain yield in rice.
GP00000218
P0046G12.12-1
Q67UU9
Morphology
replacement of a 637bp stretch of the middle of exon5 by a 12-bp sequence creating a premature stop codon and consequently a loss of 230 residues from the C-terminus N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
DEP1
Oryza sativa
rice - (species)
Published - Accepted by Curator
DEP1 (DENSE AND ERECT PANICLES 1)
Nitrogen use (metabolism)
Coding,
SNP
Oryza sativa Japonica Group
Japanese rice - (no rank)
Domesticated
Linkage Mapping
Sun H; Qian Q; Wu K ; et al. (2014)
Heterotrimeric G proteins regulate nitrogen-use efficiency in rice.
GP00001376
P0046G12.12-1
Q67UU9
Physiology
p.Cys105Tyr affecting affinity interaction between the GGL domain of DEP1 and RGB1 subunit
Oryza sativa Indica Group
long-grained rice - (no rank)
Oryza sativa Japonica Group
Japanese rice - (no rank)
DEP1 (DENSE AND ERECT PANICLES 1)
Oryza sativa Japonica Group
Japanese rice - (no rank)
Published - Accepted by Curator
diacylglycerol acyltransferase 1 (DGAT1)
Milk fat content
Coding,
SNP
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Grisart B; Coppieters W; Farnir F ; et al. (2002)
Positional candidate cloning of a QTL in dairy cattle: identification of a missense mutation in the [...]
1 Additional References
GP00000222
Dgat1
Q9Z2A7
Physiology
K232A
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
diacylglycerol acyltransferase 1 (DGAT1)
Bos taurus
cattle - (species)
Published - Accepted by Curator
diacylglycerol acyltransferase 1-2 (DGAT1-2)
Oil composition
Oil yield
Coding,
Deletion
Zea mays
(species) D
Domesticated
Linkage Mapping
Zheng P; Allen WB; Roesler K ; et al. (2008)
A phenylalanine in DGAT is a key determinant of oil content and composition in maize.
GP00000223
DGAT1-2
B0LF77
Physiology
Physiology
Deletion of amino acid F469
Zea mays
(species)
Zea mays
(species) D
diacylglycerol acyltransferase 1-2 (DGAT1-2)
Zea mays
(species)
Published - Accepted by Curator
dihydroflavonol reductase (DFR)
Coloration (tuber skin)
Coding,
Unknown
Solanum tuberosum
potato - (species)
Domesticated
Linkage Mapping
De Jong WS; De Jong DM; De Jong H ; et al. (2003)
An allele of dihydroflavonol 4-reductase associated with the ability to produce red anthocyanin pigm[...]
1 Additional References
GP00000226
DFRA
P51102
Morphology
unknown; 10 a.a variable positions
Solanum tuberosum
potato - (species)
Solanum tuberosum
potato - (species)
dihydroflavonol reductase (DFR)
Solanum tuberosum
potato - (species)
Published - Accepted by Curator
Distal-less
Coloration (wing)
Cis-regulatory,
Unknown
Bicyclus anynana
squinting bush brown - (species)
Domesticated
Linkage Mapping
Beldade P; Brakefield PM; Long AD (2002)
Contribution of Distal-less to quantitative variation in butterfly eyespots.
GP00000229
Dll
P20009
Morphology
unknown
Bicyclus anynana
squinting bush brown - (species)
Bicyclus anynana
squinting bush brown - (species)
Distal-less
Bicyclus anynana
squinting bush brown - (species)
Published - Accepted by Curator
DMRT3
Gait (ability to pace)
Coding,
SNP
N
Equus caballus
horse - (species)
Domesticated
Linkage Mapping
Andersson LS; Larhammar M; Memic F ; et al. (2012)
Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice.
1 Additional References
GP00000230
DMRT3
F6W2R2
Behavior
g.22999655C>A p.S301* Premature stop codon (Ser301Stop) resulting in truncated protein: a single base change at nucleotide position chr23:22999655 causing a premature stop at codon 301 in DMRT3 (DMRT3_Ser301STOP). The allele is expected to encode a truncated protein lacking 1 N
Equus caballus
horse - (species)
Equus caballus
horse - (species)
DMRT3
Equus caballus
horse - (species)
Published - Accepted by Curator
ds1
Pathogen resistance
Unknown,
Unknown
Sorghum bicolor
sorghum - (species)
Domesticated
Linkage Mapping
Kawahigashi H; Kasuga S; Ando T ; et al. (2011)
Positional cloning of ds1, the target leaf spot resistance gene against Bipolaris sorghicola in sorg[...]
GP00000238
ds1
K0IXC4
Physiology
unknown
Sorghum bicolor
sorghum - (species)
Sorghum bicolor
sorghum - (species)
ds1
Sorghum bicolor
sorghum - (species)
Published - Accepted by Curator
DTH2
Flowering time
2 Mutations:
Coding
SNP
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Wu W; Zheng XM; Lu G ; et al. (2013)
Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cult[...]
GP00000239
DTH2
O82118
Physiology
2 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
DTH2
Oryza sativa
rice - (species)
Published - Accepted by Curator
Dvl2
Organ size (tail)
Coding,
Deletion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Mansour TA; Lucot K; Konopelski SE ; et al. (2018)
Whole genome variant association across 100 dogs identifies a frame shift mutation in DISHEVELLED 2 [...]
GP00002110
DVL2
O14641
Morphology
single base deletion found on CFA 5(g.32195043_32195044del) that is homozygous in the three screw tail breeds - predicted to lead to a frameshift mutation and cause a premature stop codon that truncates the translated protein by 23 amino acids (p.Pro684LeufsX26) - 26 altered amino acids are predicted to be present in the highly conserved C-terminus of the mutant protein. N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
Dvl2
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
dwarf-8 (d8)
Plant size (dwarfism)
Coding,
Deletion
N
Zea mays
(species) D
Domesticated
Linkage Mapping
Peng J; Richards DE; Hartley NM ; et al. (1999)
'Green revolution' genes encode mutant gibberellin response modulators.
2 Additional References
GP00000241
D8
Q9ST48
Morphology
330bp deletion to V84 N
Zea mays
(species)
Zea mays
(species) D
dwarf-8 (d8)
Zea mays
(species)
Published - Accepted by Curator
E2F1
Silk yield
Cis-regulatory,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Association Mapping
Tong X; Han MJ; Lu K ; et al. (2022)
High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecologic[...]
GP00002400
E2f1
Q27368
Physiology
There are one deletion and three insertions in the cis-regulatory region and introns of the E2F1 gene of the improved strain. Higher expression in the improves strain. CRISPR-cas9 mediated knockout of BmE2F1 reduces the number of silk gland cells by 7.68% and silk yield by 22%.
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
E2F1
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
EARLY FLOWERING 3 (here = Mat-a)
Flowering time
Coding,
Deletion
N
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Zakhrabekova S; Gough SP; Braumann I ; et al. (2012)
Induced mutations in circadian clock regulator Mat-a facilitated short-season adaptation and range e[...]
GP00000243
ELF3
O82804
Physiology
4bp deletion resulting in truncated protein ; this deletion seem to have evolved multiple times (fragile site?) N
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
EARLY FLOWERING 3 (here = Mat-a)
Hordeum vulgare
(species)
Published - Accepted by Curator
EARLY FLOWERING 3(ELF3)
Flowering time (latitudinal adaptation)
Coding,
Deletion
N
Glycine max
soybean - (species) D
Domesticated
Linkage Mapping
Lu S; Zhao X; Hu Y ; et al. (2017)
Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield.
GP00001683
CYP75B1
Q9SD85
Physiology
recessive allele responsible for the LJ trait - 10-bp deletion predicted to cause a frameshift resulting in premature termination of translation after 195 amino acids in the 714-amino-acid protein N
Glycine max
soybean - (species)
Glycine max
soybean - (species) D
EARLY FLOWERING 3(ELF3)
Glycine max
soybean - (species)
Published - Accepted by Curator
EARLY FLOWERING 3/ EARLY MATURITY 8
Flowering time
Coding,
SNP
N
Hordeum vulgare
(species)
Domesticated
Linkage Mapping
Faure S; Turner AS; Gruszka D ; et al. (2012)
Mutation at the circadian clock gene EARLY MATURITY 8 adapts domesticated barley (Hordeum vulgare) t[...]
GP00000245
ELF3
O82804
Physiology
Premature stop codon; C-to-T point mutation in exon 2 N
Hordeum vulgare
(species)
Hordeum vulgare
(species)
EARLY FLOWERING 3/ EARLY MATURITY 8
Hordeum vulgare
(species)
Published - Accepted by Curator
EARLY FLOWERING 3/ EARLYMATURITY8
Flowering time
Coding,
Deletion
N
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Faure S; Turner AS; Gruszka D ; et al. (2012)
Mutation at the circadian clock gene EARLY MATURITY 8 adapts domesticated barley (Hordeum vulgare) t[...]
GP00000246
ELF3
O82804
Physiology
4bp deletion resulting in truncated protein ; this deletion seem to have evolved multiple times (fragile site?) N
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
EARLY FLOWERING 3/ EARLYMATURITY8
Hordeum vulgare
(species)
Published - Accepted by Curator
EARLY FLOWERING 3/Hd17
Flowering time
Unknown,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Matsubara K; Ogiso-Tanaka E; Hori K ; et al. (2012)
Natural variation in Hd17, a homolog of Arabidopsis ELF3 that is involved in rice photoperiodic flow[...]
GP00000247
ELF3
O82804
Physiology
unknown
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
EARLY FLOWERING 3/Hd17
Oryza sativa
rice - (species)
Published - Accepted by Curator
Early flowering1 (EL1)
Flowering time (heading date)
Coding,
SNP
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Domesticated
Linkage Mapping
Kwon CT; Yoo SC; Koo BH ; et al. (2014)
Natural variation in Early flowering1 contributes to early flowering in japonica rice under long day[...]
GP00001636
HD16
Q852L0
Physiology
G476C p.Gly159Ala in the serine/threonine kinase domain leading to non-functional protein
Oryza sativa
rice - (species)
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Early flowering1 (EL1)
Oryza sativa Japonica Group
Japanese rice - (no rank)
Published - Accepted by Curator
Early flowering1 (EL1)
Flowering time (heading date)
Coding,
SNP
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Domesticated
Linkage Mapping
Kwon CT; Yoo SC; Koo BH ; et al. (2014)
Natural variation in Early flowering1 contributes to early flowering in japonica rice under long day[...]
GP00001637
HD16
Q852L0
Physiology
G991A p.Ala331Thr in the serine/threonine kinase domain leading to non-functional protein
Oryza sativa
rice - (species)
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Early flowering1 (EL1)
Oryza sativa Japonica Group
Japanese rice - (no rank)
Published - Accepted by Curator
Ecdysone oxidase
Developmental time
Cis-regulatory,
Insertion
Bombyx mori
domestic silkworm - (species) D
Domesticated
Candidate Gene
Sun W; Shen YH; Han MJ ; et al. (2014)
An adaptive transposable element insertion in the regulatory region of the EO gene in the domesticat[...]
1 Additional References
GP00001102
Eo
Q9VY01
Physiology
insertion of a 512bp fragment of a Taguchi transposable element 462 bp upstream of the transcription start site of the EO gene. The TE insertion enhances the transcription of flanking genes after 20-hydroxyecdysone treatment.
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Ecdysone oxidase
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
EDN3
Coloration (hyperpigmentation)
Gene Amplification,
Complex Change
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Dorshorst B; Molin AM; Rubin CJ ; et al. (2011)
A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in [...]
3 Additional References
GP00000258
EDN3
P14138
Morphology
Large duplication
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
EDN3
Gallus gallus
chicken - (species)
Published - Accepted by Curator
EDN3
Coloration (coat)
Coloration (eyes)
Hearing (loss)
Unknown,
Unknown
Lama glama
llama - (species) D
Vicugna pacos
alpaca - (species) D
Domesticated
Candidate Gene
Fan R; Gu Z; Guang X ; et al. (2020)
Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca.
GP00002182
EDN3
P14138
Morphology
Morphology
Physiology
Introgression from alpacas to lamas and clear correlation wit phenotype but no information on the mutation(s)
Vicugna vicugna
vicugna - (species)
Lama glama
llama - (species) D
Vicugna pacos
alpaca - (species) D
EDN3
Lama glama
llama - (species)
Vicugna pacos
alpaca - (species)
Published - Accepted by Curator
EDN3
Coloration
Cis-regulatory,
Unknown
Ambystoma mexicanum
axolotl - (species) D
Domesticated
Candidate Gene
Woodcock MR; Vaughn-Wolfe J; Elias A ; et al. (2017)
Identification of Mutant Genes and Introgressed Tiger Salamander DNA in the Laboratory Axolotl, Amby[...]
GP00002377
EDN3
P14138
Morphology
Ambystoma mexicanum
axolotl - (species)
Ambystoma mexicanum
axolotl - (species) D
EDN3
Ambystoma mexicanum
axolotl - (species)
Published - Accepted by Curator
EDNRA
Coloration (coat ; white-spotting)
Gene Amplification,
Insertion
Capra hircus
goat - (species) D
Domesticated
Association Mapping
Menzi F; Keller I; Reber I ; et al. (2016)
Genomic amplification of the caprine EDNRA locus might lead to a dose dependent loss of pigmentation[...]
GP00002170
Ednra
Q61614
Morphology
1 Mb copy number variant (CNV) harboring 5 genes including EDNRA ; The duplicated EDNRA copies contain a missense variant (p.Tyr129His) predicted to increase the affinity of the encoded mutant receptor for endothelin 3. Menzi et al. proposed a hypothesis whereby ectopic overexpression of a mutant EDNRA scavenges EDN3 required for EDNRB signaling and normal melanocyte development and thus likely leads to an absence of melanocytes in the non-pigmented body areas of Boer goats (thanks to OMIA for the summary)
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
EDNRA
Capra hircus
goat - (species)
Published - Accepted by Curator
Ehd1 (Response regulator)
Flowering time
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Doi K; Izawa T; Fuse T ; et al. (2004)
Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-[...]
GP00000263
EHD1
Q9H4M9
Physiology
G218R in highly conserved region in GARP domain
Oryza glaberrima
African rice - (species)
Oryza sativa
rice - (species)
Ehd1 (Response regulator)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Endothelin receptor B
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Metallinos DL; Bowling AT; Rine J (1998)
A missense mutation in the endothelin-B receptor gene is associated with Lethal White Foal Syndrome:[...]
2 Additional References
GP00000269
Ednrb
P48302
Morphology
Ile118Lys
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Endothelin receptor B
Equus caballus
horse - (species)
Published - Accepted by Curator
Endothelin receptor B
Coloration (feathers ; white-spotting)
Coding,
SNP
Coturnix japonica
Japanese quail - (species) D
Domesticated
Linkage Mapping
Miwa M; Inoue-Murayama M; Aoki H ; et al. (2007)
Endothelin receptor B2 (EDNRB2) is associated with the panda plumage colour mutation in Japanese qua[...]
GP00000270
Ednrb
P48302
Morphology
c.995G>A p.R332H
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species) D
Endothelin receptor B
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
Endothelin receptor B2
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Kinoshita K; Akiyama T; Mizutani M ; et al. (2014)
Endothelin receptor B2 (EDNRB2) is responsible for the tyrosinase-independent recessive white (mo(w)[...]
GP00001360
EDNRB2
W8VUK4
Morphology
c.1008G>T p.Cys244Phe
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Endothelin receptor B2
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Endothelin receptor B2
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Kinoshita K; Akiyama T; Mizutani M ; et al. (2014)
Endothelin receptor B2 (EDNRB2) is responsible for the tyrosinase-independent recessive white (mo(w)[...]
GP00001361
EDNRB2
W8VUK4
Morphology
c.G1272A p.Arg332His
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Endothelin receptor B2
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Endothelin receptor B2
Coloration (feathers ; white-spotting)
Coding,
SNP
Anas platyrhynchos
mallard - (species) D
Domesticated
Candidate Gene
Li L; Li D; Liu L ; et al. (2015)
Endothelin Receptor B2 (EDNRB2) Gene Is Associated with Spot Plumage Pattern in Domestic Ducks (Anas[...]
GP00002378
EDNRB2
W8VUK4
Morphology
Anas platyrhynchos
mallard - (species)
Anas platyrhynchos
mallard - (species) D
Endothelin receptor B2
Anas platyrhynchos
mallard - (species)
Published - Accepted by Curator
Endothelin receptor B2
Coloration (feathers ; white-spotting)
Cis-regulatory,
Unknown
Anas platyrhynchos
mallard - (species) D
Domesticated
Association Mapping
Xi Y; Xu Q; Huang Q ; et al. (2021)
Genome-wide association analysis reveals that EDNRB2 causes a dose-dependent loss of pigmentation in[...]
GP00002383
EDNRB2
W8VUK4
Morphology
"The GWAS results identified a 198 kb (Chr4: 10,149,651 bp to 10,348,068 bp) genetic region that was significantly associated with the black spot phenotype. The conditional GWAS and linkage disequilibrium (LD) analysis further narrowed the ultimate candidate region to 167 kb (Chr4: 10,180,939 bp to 10,348,068 bp). A key gene regulating melanoblast migration and differentiation, EDNRB2 (Endothelin B receptor-like), was found in the candidate region and having significant mRNA expression level changes in embryonic duck skin tissue with different spot sizes. The significant SNPs (single nucleotide polymorphisms) associated with the EDNRB2 gene were annotated, and two mutations (Chr4: 10,180,939 T > C and Chr4: 10,190,671 A > T) were found to result in the loss of binding sites for two trans-factors, XBP1 and cMYB. The phenotypic effect of these two mutations suggested that they can regulate the size of black spots in a dose-dependent manner, and Chr4: 10,180,939 T > C was the major allele locus."
Anas platyrhynchos
mallard - (species)
Anas platyrhynchos
mallard - (species) D
Endothelin receptor B2
Anas platyrhynchos
mallard - (species)
Published - Accepted by Curator
EOMES (eomesodermin)
Bird head comb (reduced)
Gene Amplification,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Dorshorst B; Harun-Or-Rashid M; Bagherpoor AJ ; et al. (2015)
A genomic duplication is associated with ectopic eomesodermin expression in the embryonic chicken co[...]
GP00000271
Eomes
O54839
Morphology
a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream of the eomesodermin gene
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
EOMES (eomesodermin)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
EphB2
Feathers (crest morphology)
Coding,
SNP
Columba livia
rock pigeon - (species) D
Domesticated
Association Mapping
Shapiro MD; Kronenberg Z; Li C ; et al. (2013)
Genomic diversity and evolution of the head crest in the rock pigeon.
1 Additional References
GP00000275
EPHB2
P28693
Morphology
Arg758Cys (C>T) p.R758C
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
EphB2
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
EphB2
Feathers (crest morphology)
Coding,
SNP
Streptopelia risoria
ringneck dove - (species) D
Domesticated
Candidate Gene
Vickrey AI; Domyan ET; Horvath MP ; et al. (2015)
Convergent Evolution of Head Crests in Two Domesticated Columbids Is Associated with Different Misse[...]
GP00000276
EPHB2
P28693
Morphology
Gly636Arg (G>A)
Streptopelia risoria
ringneck dove - (species)
Streptopelia risoria
ringneck dove - (species) D
EphB2
Streptopelia risoria
ringneck dove - (species)
Published - Accepted by Curator
FAD2 (BnaA.FAD2.a)
Oil composition
Oil yield
Coding,
Insertion
N
Brassica napus
rape - (species) D
Domesticated
Linkage Mapping
Yang Q; Fan C; Guo Z ; et al. (2012)
Identification of FAD2 and FAD3 genes in Brassica napus genome and development of allele-specific ma[...]
GP00000302
FAD2
P46313
Physiology
Physiology
4bp insertion resulting in frameshift and premature stop codon N
Brassica napus
rape - (species)
Brassica napus
rape - (species) D
FAD2 (BnaA.FAD2.a)
Brassica napus
rape - (species)
Published - Accepted by Curator
FAD2A
Oil composition (oleate levels)
Coding,
SNP
N
Arachis hypogaea
peanut - (species) D
Domesticated
Candidate Gene
Jung S; Powell G; Moore K ; et al. (2000)
The high oleate trait in the cultivated peanut [Arachis hypogaea L]. II. Molecular basis and genetic[...]
GP00002075
FAD2A
E2GJC1
Physiology
D150N in a residue that is absolutely conserved among other desaturases N
Arachis hypogaea
peanut - (species)
Arachis hypogaea
peanut - (species) D
FAD2A
Arachis hypogaea
peanut - (species)
Published - Accepted by Curator
FAD2B
Oil composition (oleate levels)
Coding,
Insertion
N
Arachis hypogaea
peanut - (species) D
Domesticated
Candidate Gene
Patel M; Jung S; Moore K ; et al. (2004)
High-oleate peanut mutants result from a MITE insertion into the FAD2 gene.
GP00002073
FAD2B
Q9LKK6
Physiology
insertion of 205-bp miniature inverted-repeat transposable element (MITE) called ahMITE1 at position 665 near the center of the coding region in the case of MF; which causes a frameshift N
Arachis hypogaea
peanut - (species)
Arachis hypogaea
peanut - (species) D
FAD2B
Arachis hypogaea
peanut - (species)
Published - Accepted by Curator
FAD2B
Oil composition (oleate levels)
Coding,
Insertion
N
Arachis hypogaea
peanut - (species) D
Domesticated
Candidate Gene
Patel M; Jung S; Moore K ; et al. (2004)
High-oleate peanut mutants result from a MITE insertion into the FAD2 gene.
GP00002074
FAD2B
Q9LKK6
Physiology
insertion of 205-bp miniature inverted-repeat transposable element (MITE) called ahMITE1 at position 997 of the coding region; which causes a frameshift N
Arachis hypogaea
peanut - (species)
Arachis hypogaea
peanut - (species) D
FAD2B
Arachis hypogaea
peanut - (species)
Published - Accepted by Curator
FaO-methyl-transferase (FaOMT)
Fragrance (flavor)
Cis-regulatory,
Unknown
Fragaria x ananassa
strawberry - (species)
Domesticated
Linkage Mapping
Zorrilla-Fontanesi Y; Rambla JL; Cabeza A ; et al. (2012)
Genetic analysis of strawberry fruit aroma and identification of O-methyltransferase FaOMT as the lo[...]
GP00000303
omt1
Q9M602
Physiology
Promoter variation _ there are several single nucleotide polymorphisms (SNPs); insertion/deletions (indels); and rearrangements in the promoter
Fragaria x ananassa
strawberry - (species)
Fragaria x ananassa
strawberry - (species)
FaO-methyl-transferase (FaOMT)
Fragaria x ananassa
strawberry - (species)
Published - Accepted by Curator
fasciated
Fruit size
Fruit architecture
Cis-regulatory,
Unknown
Solanum lycopersicum
tomato - (species)
Domesticated
Linkage Mapping
Cong B; Barrero LS; Tanksley SD (2008)
Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during t[...]
GP00000305
fasciated
B2YHV8
Morphology
Morphology
Possibly 7-bp and 6- to 8-kb insertion in the first intron
Solanum pennellii
(species)
Solanum lycopersicum
tomato - (species)
fasciated
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
FASCIATED EAR2
Grain yield (kernel row number)
Unknown,
Unknown
Zea mays
(species)
Domesticated
Linkage Mapping
Bommert P; Nagasawa NS; Jackson D (2013)
Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus.
GP00000306
FEA2
Q940E8
Morphology
Not identified
Zea mays
(species)
Zea mays
(species)
FASCIATED EAR2
Zea mays
(species)
Published - Accepted by Curator
FGF20
Organ loss (feathers ; scales)
Coding,
SNP
N
Gallus gallus
chicken - (species) D
Domesticated
Association Mapping
Wells KL; Hadad Y; Ben-Avraham D ; et al. (2012)
Genome-wide SNP scan of pooled DNA reveals nonsense mutation in FGF20 in the scaleless line of feath[...]
GP00002171
FGF20
Q9NP95
Morphology
g.62878803A>T c.535A>T p.R179* N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
FGF20
Gallus gallus
chicken - (species)
Published - Accepted by Curator
FGF3; FGF4; FGF19; ORAOV1
Coloration (coat; dog Ridgeback phenotype)
Gene Amplification,
Complex Change
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Linkage Mapping
Salmon Hillbertz NH; Isaksson M; Karlsson EK ; et al. (2007)
Duplication of FGF3, FGF4, FGF19 and ORAOV1 causes hair ridge and predisposition to dermoid sinus in[...]
GP00000308
FGF4
J9P3I7
Morphology
Gene duplication
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF3; FGF4; FGF19; ORAOV1
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF4 retrogene
Limb size
Unknown,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Parker HG; VonHoldt BM; Quignon P ; et al. (2009)
An expressed fgf4 retrogene is associated with breed-defining chondrodysplasia in domestic dogs.
GP00000309
FGF4
J9P3I7
Morphology
Gene retroposition : 5kb insertion containing a FGF4 retrogene; 25Mb away from the complete (original) FGF4 gene
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF4 retrogene
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Cadieu E; Neff MW; Quignon P ; et al. (2009)
Coat variation in the domestic dog is governed by variants in three genes.
GP00000310
Fgf5
P15656
Morphology
Cys95Phe
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF5
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF5
Hair length (length)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Drögemüller C; Rüfenacht S; Wichert B ; et al. (2007)
Mutations within the FGF5 gene are associated with hair length in cats.
1 Additional References
GP00000311
Fgf5
P15656
Morphology
c.474delT resulting in frameshift N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
FGF5
Felis catus
domestic cat - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Deletion
N
Equus asinus
ass - (species) D
Domesticated
Candidate Gene
Legrand R; Tiret L; Abitbol M (2014)
Two recessive mutations in FGF5 are associated with the long-hair phenotype in donkeys.
GP00001369
Fgf5
P15656
Morphology
c.433_434delAT frameshift deletion leading to a stop codon at position 159 N
Equus asinus
ass - (species)
Equus asinus
ass - (species) D
FGF5
Equus asinus
ass - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
N
Equus asinus
ass - (species) D
Domesticated
Candidate Gene
Legrand R; Tiret L; Abitbol M (2014)
Two recessive mutations in FGF5 are associated with the long-hair phenotype in donkeys.
GP00001370
Fgf5
P15656
Morphology
c.245G>A p.W82* nonsense mutation leading to stop codon at position 82 N
Equus asinus
ass - (species)
Equus asinus
ass - (species) D
FGF5
Equus asinus
ass - (species)
Published - Accepted by Curator
FGF5
Hair length (length)
Coding,
Insertion
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Drögemüller C; Rüfenacht S; Wichert B ; et al. (2007)
Mutations within the FGF5 gene are associated with hair length in cats.
1 Additional References
GP00002172
Fgf5
P15656
Morphology
c.ins356T resulting in frameshift N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
FGF5
Felis catus
domestic cat - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Deletion
N
Mesocricetus auratus
golden hamster - (species) D
Domesticated
Candidate Gene
Yoshizawa Y; Wada K; Shimoi G ; et al. (2015)
A 1-bp deletion in Fgf5 causes male-dominant long hair in the Syrian hamster.
GP00002173
Fgf5
P15656
Morphology
c.546delG p.Arg184GlyfsX6 N
Mesocricetus auratus
golden hamster - (species)
Mesocricetus auratus
golden hamster - (species) D
FGF5
Mesocricetus auratus
golden hamster - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dierks C; Mömke S; Philipp U ; et al. (2013)
Allelic heterogeneity of FGF5 mutations causes the long-hair phenotype in dogs.
1 Additional References
GP00002174
Fgf5
P15656
Morphology
g.4528639C>T c.578C>T p.A193V
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF5
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dierks C; Mömke S; Philipp U ; et al. (2013)
Allelic heterogeneity of FGF5 mutations causes the long-hair phenotype in dogs.
1 Additional References
GP00002175
Fgf5
P15656
Morphology
g.8193T>A splice site
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF5
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dierks C; Mömke S; Philipp U ; et al. (2013)
Allelic heterogeneity of FGF5 mutations causes the long-hair phenotype in dogs.
1 Additional References
GP00002176
Fgf5
P15656
Morphology
c.559_560dupGG p.R188Afs*73
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF5
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Deletion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dierks C; Mömke S; Philipp U ; et al. (2013)
Allelic heterogeneity of FGF5 mutations causes the long-hair phenotype in dogs.
1 Additional References
GP00002177
Fgf5
P15656
Morphology
c.556_571del16 p.A186Tfs*69
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FGF5
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
N
Cavia porcellus
domestic guinea pig - (species) D
Domesticated
Candidate Gene
Yu F; Liu Z; Jiao S ; et al. (2018)
A nonsense mutation in the FGF5 gene is associated with the long-haired phenotype in domestic guinea[...]
GP00002178
Fgf5
P15656
Morphology
c.403C>T p.Arg135* N
Cavia porcellus
domestic guinea pig - (species)
Cavia porcellus
domestic guinea pig - (species) D
FGF5
Cavia porcellus
domestic guinea pig - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Indel
N
Lama glama
llama - (species) D
Domesticated
Candidate Gene
Daverio MS; Vidal-Rioja L; Frank EN ; et al. (2017)
Molecular characterization of the llama FGF5 gene and identification of putative loss of function mu[...]
GP00002179
Fgf5
P15656
Morphology
a single base deletion (c.348delA) + a 12-bp insertion (c.351_352insCATATAACATAG) N
Lama guanicoe
guanaco - (species)
Lama glama
llama - (species) D
FGF5
Lama glama
llama - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
N
Lama glama
llama - (species) D
Vicugna pacos
alpaca - (species) D
Domesticated
Candidate Gene
Daverio MS; Vidal-Rioja L; Frank EN ; et al. (2017)
Molecular characterization of the llama FGF5 gene and identification of putative loss of function mu[...]
2 Additional References
GP00002180
Fgf5
P15656
Morphology
transition C>T at position 499 downstream of the ATG codon with transcriptional readthrough ; difference in post-transcriptional readthrough may underlie the different fleece types of the alpaca suri and huacaya breeds ; derived allele was introgressed from lamas to alpacas N
Lama guanicoe
guanaco - (species)
Lama glama
llama - (species) D
Vicugna pacos
alpaca - (species) D
FGF5
Lama glama
llama - (species)
Vicugna pacos
alpaca - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Deletion
N
Mus musculus
house mouse - (species) D
Domesticated
Candidate Gene
Hébert JM; Rosenquist T; Götz J ; et al. (1994)
FGF5 as a regulator of the hair growth cycle: evidence from targeted and spontaneous mutations.
1 Additional References
GP00002441
Fgf5
P15656
Morphology
Deletion which extends at least 2kb upstream of the Fgf5 translational start site and terminates at the end of the first exon or beginning of the first intron. N
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species) D
FGF5
Mus musculus
house mouse - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
Deletion
N
Mus musculus
house mouse - (species) D
Domesticated
Candidate Gene
Mizuno S; Iijima S; Okano T ; et al. (2011)
Retrotransposon-mediated Fgf5(go-Utr) mutant mice with long pelage hair.
GP00002442
Fgf5
P15656
Morphology
Deletion of a 9.3-kb region in the Fgf5 gene including exon 3 and its 5' and 3' flanking sequences. The genomic deletion site also shows insertion of a 498-bp early transposon element long terminal repeat. N
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species) D
FGF5
Mus musculus
house mouse - (species)
Published - Accepted by Curator
FGF5
Hair length
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Housley DJ; Venta PJ (2006)
The long and the short of it: evidence that FGF5 is a major determinant of canine 'hair'-itability.
GP00002443
Fgf5
P15656
Morphology
Presence of a duplication in a relatively non-conserved region of the gene and a missense mutation resulting in the substitution of Phe for Cys in a highly conserved region. Genotyping of 218 dogs from three breeds fixed for long hair; eight breeds fixed for short hair and five breeds in which long hair is segregating provided evidence that the missense mutation is associated with the hair-length differences among these breeds.
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
FGF5
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Fgfr1a1
Scales (loss)
Coding,
Deletion
N
Cyprinus carpio
common carp - (species) D
Domesticated
Candidate Gene
Rohner N; Bercsényi M; Orbán L ; et al. (2009)
Duplication of fgfr1 permits Fgf signaling to serve as a target for selection during domestication.
GP00000312
fgfr1a
Q90Z00
Morphology
deletion of 310 bp N
Cyprinus carpio
common carp - (species)
Cyprinus carpio
common carp - (species) D
Fgfr1a1
Cyprinus carpio
common carp - (species)
Published - Accepted by Curator
Fgfr1a1
Scales (loss)
Coding,
SNP
Cyprinus carpio
common carp - (species) D
Domesticated
Candidate Gene
Rohner N; Bercsényi M; Orbán L ; et al. (2009)
Duplication of fgfr1 permits Fgf signaling to serve as a target for selection during domestication.
GP00000313
fgfr1a
Q90Z00
Morphology
Glu664Lys
Cyprinus carpio
common carp - (species)
Cyprinus carpio
common carp - (species) D
Fgfr1a1
Cyprinus carpio
common carp - (species)
Published - Accepted by Curator
FGFR3
Body size (bone length)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Beever JE; Smit MA; Meyers SN ; et al. (2006)
A single-base change in the tyrosine kinase II domain of ovine FGFR3 causes hereditary chondrodyspla[...]
1 Additional References
GP00002184
FGFR3
P22607
Morphology
c.1719T>A p.V700E
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
FGFR3
Ovis aries
sheep - (species)
Published - Accepted by Curator
Fkh
Silk yield
Cis-regulatory,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Association Mapping
Xia Q; Guo Y; Zhang Z ; et al. (2009)
Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).
GP00002411
fkh
P14734
Physiology
Increased expression in high yield strains. The Fkh gene encodes a transcription factor that activates glue genes together with Sage in salivary glands of Drosophila melanogaster.
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Fkh
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers)
Cis-regulatory,
Insertion
Glycine max
soybean - (species) D
Domesticated
Candidate Gene
Zabala G; Vodkin LO (2005)
The wp mutation of Glycine max carries a gene-fragment-rich transposon of the CACTA superfamily.
GP00000318
CYP75B1
Q9SD85
Morphology
Transposon insertion in intron 2
Glycine max
soybean - (species)
Glycine max
soybean - (species) D
flavonoid 3'-hydroxylase (F3'H)
Glycine max
soybean - (species)
Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers)
Coding,
Insertion
N
Ipomoea purpurea
common morning-glory - (species) D
Domesticated
Candidate Gene
Zufall RA; Rausher MD (2003 Nov-Dec)
The genetic basis of a flower color polymorphism in the common morning glory (Ipomoea purpurea).
3 Additional References
GP00000319
CYP75B1
Q9SD85
Morphology
insertion of the 0.55-kb DNA transposable element Tip201 belonging to the Ac/Ds superfamily. No excision of Tip201 from the F3'H gene could be detected. Both splicing and polyadenylation patterns of the F3'H transcripts were affected by the Tip201 integration. N
Ipomoea purpurea
common morning-glory - (species)
Ipomoea purpurea
common morning-glory - (species) D
flavonoid 3'-hydroxylase (F3'H)
Ipomoea purpurea
common morning-glory - (species)
Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers)
Unknown,
Unknown
Petunia x hybrida
(species)
Domesticated
Candidate Gene
Brugliera F; Barri-Rewell G; Holton TA ; et al. (1999)
Isolation and characterization of a flavonoid 3'-hydroxylase cDNA clone corresponding to the Ht1 loc[...]
GP00000320
CYP75B1
Q9SD85
Morphology
Not identified
Petunia x hybrida
(species)
Petunia x hybrida
(species)
flavonoid 3'-hydroxylase (F3'H)
Petunia x hybrida
(species)
Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)
Coloration (seed; pods)
Coding,
Deletion
N
Glycine max
soybean - (species) D
Domesticated
Linkage Mapping
Toda K; Yang D; Yamanaka N ; et al. (2002)
A single-base deletion in soybean flavonoid 3'-hydroxylase gene is associated with gray pubescence c[...]
1 Additional References
GP00000321
CYP75B1
Q9SD85
Morphology
1bp deletion resulting in frameshift N
Glycine max
soybean - (species)
Glycine max
soybean - (species) D
flavonoid 3'-hydroxylase (F3'H)
Glycine max
soybean - (species)
Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers)
Coding,
SNP
N
Ipomoea nil
Japanese morning glory - (species) D
Domesticated
Candidate Gene
Hoshino A; Morita Y; Choi JD ; et al. (2003)
Spontaneous mutations of the flavonoid 3'-hydroxylase gene conferring reddish flowers in the three m[...]
GP00002087
CYP75B1
Q9SD85
Morphology
nonsense mutation caused by a single C to T base transition generating the stop codon TGA. N
Ipomoea nil
Japanese morning glory - (species)
Ipomoea nil
Japanese morning glory - (species) D
flavonoid 3'-hydroxylase (F3'H)
Ipomoea nil
Japanese morning glory - (species)
Published - Accepted by Curator
flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers)
Coding,
Insertion
N
Ipomoea tricolor
(species) D
Domesticated
Candidate Gene
Hoshino A; Morita Y; Choi JD ; et al. (2003)
Spontaneous mutations of the flavonoid 3'-hydroxylase gene conferring reddish flowers in the three m[...]
GP00002088
CYP75B1
Q9SD85
Morphology
a single T insertion generating the stop codon TAG. The accumulation of the F3'H transcripts is drastically reduced by the nonsense-mediated RNA decay. N
Ipomoea tricolor
(species)
Ipomoea tricolor
(species) D
flavonoid 3'-hydroxylase (F3'H)
Ipomoea tricolor
(species)
Published - Accepted by Curator
flavonoid 3';5'-hydroxylase (F3'5'H)
Coloration (flowers)
Coding,
SNP
Pisum sativum
pea - (species)
Domesticated
Candidate Gene
Moreau C; Ambrose MJ; Turner L ; et al. (2012)
The B gene of pea encodes a defective flavonoid 3',5'-hydroxylase, and confers pink flower color.
GP00000326
CYP75A2
P37120
Morphology
G111E
Pisum sativum
pea - (species)
Pisum sativum
pea - (species)
flavonoid 3';5'-hydroxylase (F3'5'H)
Pisum sativum
pea - (species)
Published - Accepted by Curator
flavonoid 3';5'-hydroxylase (F3'5'H)
Coloration (flowers)
Coding,
Deletion
N
Pisum sativum
pea - (species) D
Domesticated
Linkage Mapping
Moreau C; Ambrose MJ; Turner L ; et al. (2012)
The B gene of pea encodes a defective flavonoid 3',5'-hydroxylase, and confers pink flower color.
GP00000327
CYP75A2
P37120
Morphology
23bp deletion reuslting in frameshift and truncated protein N
Pisum sativum
pea - (species)
Pisum sativum
pea - (species) D
flavonoid 3';5'-hydroxylase (F3'5'H)
Pisum sativum
pea - (species)
Published - Accepted by Curator
flavonoid 3';5'-hydroxylase (F3'5'H)
Coloration (tuber skin)
Cis-regulatory,
Unknown
Solanum tuberosum
potato - (species)
Domesticated
Linkage Mapping
Jung CS; Griffiths HM; De Jong DM ; et al. (2005)
The potato P locus codes for flavonoid 3',5'-hydroxylase.
GP00000328
CYP75A2
P37120
Morphology
unknown
Solanum tuberosum
potato - (species)
Solanum tuberosum
potato - (species)
flavonoid 3';5'-hydroxylase (F3'5'H)
Solanum tuberosum
potato - (species)
Published - Accepted by Curator
FLC-1
Flowering time
Coding,
SNP
Brassica rapa
field mustard - (species)
Domesticated
Linkage Mapping
Yuan YX; Wu J; Sun RF ; et al. (2009)
A naturally occurring splicing site mutation in the Brassica rapa FLC1 gene is associated with varia[...]
GP00000338
FLC
Q9S7Q7
Physiology
GA substitution disrupting Splice Site
Brassica rapa
field mustard - (species)
Brassica rapa
field mustard - (species)
FLC-1
Brassica rapa
field mustard - (species)
Published - Accepted by Curator
FLC-2
Flowering time
Coding,
Deletion
N
Brassica oleracea
wild cabbage - (species) D
Domesticated
Linkage Mapping
Okazaki K; Sakamoto K; Kikuchi R ; et al. (2007)
Mapping and characterization of FLC homologs and QTL analysis of flowering time in Brassica oleracea[...]
GP00000339
FLC
Q9S7Q7
Physiology
1bp deletion resulting in frameshift N
Brassica oleracea
wild cabbage - (species)
Brassica oleracea
wild cabbage - (species) D
FLC-2
Brassica oleracea
wild cabbage - (species)
Published - Accepted by Curator
FLC-2
Flowering time
Cis-regulatory,
Unknown
Brassica rapa
field mustard - (species)
Domesticated
Linkage Mapping
Zhao J; Kulkarni V; Liu N ; et al. (2010)
BrFLC2 (FLOWERING LOCUS C) as a candidate gene for a vernalization response QTL in Brassica rapa.
GP00000340
FLC
Q9S7Q7
Physiology
unknown
Brassica rapa
field mustard - (species)
Brassica rapa
field mustard - (species)
FLC-2
Brassica rapa
field mustard - (species)
Published - Accepted by Curator
FLO1
Cell separation
Other,
Unknown
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Candidate Gene
Smukalla S; Caldara M; Pochet N ; et al. (2008)
FLO1 is a variable green beard gene that drives biofilm-like cooperation in budding yeast.
1 Additional References
GP00000342
FLO1
P32768
Physiology
both coding and non-coding divergence ; polyQ variation
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
FLO1
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
Flowering locus T (=HvFT=VRN3)
Flowering time
Cis-regulatory,
Unknown
Hordeum vulgare
(species)
Domesticated
Linkage Mapping
Yan L; Fu D; Li C ; et al. (2006)
The wheat and barley vernalization gene VRN3 is an orthologue of FT.
GP00000343
FT
Q9SXZ2
Physiology
Regulatory variation in first intron
Hordeum vulgare
(species)
Hordeum vulgare
(species)
Flowering locus T (=HvFT=VRN3)
Hordeum vulgare
(species)
Published - Accepted by Curator
Flowering locus T (=TaFT=VRN3)
Flowering time
Cis-regulatory,
Insertion
Triticum aestivum
bread wheat - (species) D
Domesticated
Linkage Mapping
Yan L; Fu D; Li C ; et al. (2006)
The wheat and barley vernalization gene VRN3 is an orthologue of FT.
GP00000344
FT
Q9SXZ2
Physiology
Retrotranspostion in promoter region
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species) D
Flowering locus T (=TaFT=VRN3)
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
Flowering locus T (FT)
Flowering time
Cis-regulatory,
Unknown
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Kojima S; Takahashi Y; Kobayashi Y ; et al. (2002)
Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1[...]
1 Additional References
GP00000345
FT
Q9SXZ2
Physiology
Promoter region
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
Flowering locus T (FT)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
Flowering locus T (FT1)
Flowering time
Coding,
Deletion
N
Helianthus annuus
common sunflower - (species) D
Domesticated
Linkage Mapping
Blackman BK; Strasburg JL; Raduski AR ; et al. (2010)
The role of recently derived FT paralogs in sunflower domestication.
GP00000346
FT
Q9SXZ2
Physiology
1bp deletion; frameshift N
Helianthus annuus
common sunflower - (species)
Helianthus annuus
common sunflower - (species) D
Flowering locus T (FT1)
Helianthus annuus
common sunflower - (species)
Published - Accepted by Curator
Flowering locus T (LpFT3)
Flowering time
Cis-regulatory,
Unknown
Lolium perenne
(species)
Domesticated
Candidate Gene
Skøt L; Sanderson R; Thomas A ; et al. (2011)
Allelic variation in the perennial ryegrass FLOWERING LOCUS T gene is associated with changes in flo[...]
GP00000347
FT
Q9SXZ2
Physiology
unknown
Lolium perenne
(species)
Lolium perenne
(species)
Flowering locus T (LpFT3)
Lolium perenne
(species)
Published - Accepted by Curator
FMN1
Recombination rate
Unknown,
Unknown
Bos taurus
cattle - (species)
Domesticated
Association Mapping
Ma L; O'Connell JR; VanRaden PM ; et al. (2015)
Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.
GP00001662
FMN1
Q68DA7
Physiology
On chromosome 10. Associated SNP located upstream of the gene
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
FMN1
Bos taurus
cattle - (species)
Published - Accepted by Curator
FOXI3
Hair (hypotrichosis)
Coding,
Insertion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Drögemüller C; Karlsson EK; Hytönen MK ; et al. (2008)
A mutation in hairless dogs implicates FOXI3 in ectodermal development.
GP00000351
FOXI3
B5RHS5
Morphology
Frameshift; 7-bp duplication within exon 1 N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
FOXI3
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
FOXL2
Horns absence
Somatic sex change
Cis-regulatory,
Deletion
Capra hircus
goat - (species) D
Domesticated
Linkage Mapping
Pailhoux E; Vigier B; Chaffaux S ; et al. (2001)
A 11.7-kb deletion triggers intersexuality and polledness in goats.
2 Additional References
GP00000352
FOXL2
Q8MIP2
Morphology
Physiology
11.7 kbp deletion of mainly repetitive sequences ; Alters transcription of two flanking genes; but FOXL2 in particular is proposed as the main determinant of the phenotype
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
FOXL2
Capra hircus
goat - (species)
Published - Accepted by Curator
Frigida (BnaA.FRI.a)
Flowering time
Unknown,
Unknown
Brassica napus
rape - (species)
Domesticated
Linkage Mapping
Wang N; Qian W; Suppanz I ; et al. (2011)
Flowering time variation in oilseed rape (Brassica napus L.) is associated with allelic variation in[...]
GP00000356
FRI
P0DH90
Physiology
unknown
Brassica napus
rape - (species)
Brassica napus
rape - (species)
Frigida (BnaA.FRI.a)
Brassica napus
rape - (species)
Published - Accepted by Curator
FRM2
Xenobiotic resistance (citrinin)
Cis-regulatory,
Unknown
Saccharomyces paradoxus
(species) D
Domesticated
Association Mapping
Naranjo S; Smith JD; Artieri CG ; et al. (2015)
Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation.
GP00001311
FRM2
P37261
Physiology
mutations within 1kb in promotor region
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces paradoxus
(species) D
FRM2
Saccharomyces paradoxus
(species)
Published - Accepted by Curator
FW2.2
Fruit size
Cis-regulatory,
Unknown
Solanum lycopersicum
tomato - (species)
Domesticated
Linkage Mapping
Frary A; Nesbitt TC; Grandillo S ; et al. (2000)
fw2.2: a quantitative trait locus key to the evolution of tomato fruit size.
1 Additional References
GP00000383
ORFX
Q9LKV7
Morphology
Not identified
Lycopersicon
(subgenus)
Solanum lycopersicum
tomato - (species)
FW2.2
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
GCLM
Recombination rate
Unknown,
Unknown
Bos taurus
cattle - (species)
Domesticated
Association Mapping
Ma L; O'Connell JR; VanRaden PM ; et al. (2015)
Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.
GP00001664
GCLM
Q2T9Y6
Physiology
On chromosome 3. Associated SNP upstream of the gene
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
GCLM
Bos taurus
cattle - (species)
Published - Accepted by Curator
GCNF (NR6A1)
Vertebrae number
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Mikawa S; Morozumi T; Shimanuki S ; et al. (2007)
Fine mapping of a swine quantitative trait locus for number of vertebrae and analysis of an orphan n[...]
GP00000386
Nr6a1
Q64249
Morphology
Pro192Leu
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
GCNF (NR6A1)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
GDF7
Feathers (loss)
Cis-regulatory,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Mou C; Pitel F; Gourichon D ; et al. (2011)
Cryptic patterning of avian skin confers a developmental facility for loss of neck feathering.
GP00002185
Gdf7
P43029
Morphology
a large insertion approximately 260kb downstream from the BMP12 gene (now known as GFD7) increasing the expression of this gene in embryonic skin
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
GDF7
Gallus gallus
chicken - (species)
Published - Accepted by Curator
GDF9
Fertility (increased ovulation rate)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Silva BD; Castro EA; Souza CJ ; et al. (2011)
A new polymorphism in the Growth and Differentiation Factor 9 (GDF9) gene is associated with increas[...]
GP00000390
GDF9
O60383
Physiology
F345C
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
GDF9
Ovis aries
sheep - (species)
Published - Accepted by Curator
GDF9
Fertility (increased ovulation rate)
Coding,
SNP
Ovis aries
sheep - (species)
Domesticated
Linkage Mapping
Nicol L; Bishop SC; Pong-Wong R ; et al. (2009)
Homozygosity for a single base-pair mutation in the oocyte-specific GDF9 gene results in sterility i[...]
GP00000391
GDF9
O60383
Physiology
g.41841117A>C c.1279A>C p.S427R
Ovis aries
sheep - (species)
Ovis aries
sheep - (species)
GDF9
Ovis aries
sheep - (species)
Published - Accepted by Curator
GDF9
Fertility (increased ovulation rate)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Våge DI; Husdal M; Kent MP ; et al. (2013)
A missense mutation in growth differentiation factor 9 (GDF9) is strongly associated with litter siz[...]
1 Additional References
GP00002186
GDF9
O60383
Physiology
g.41841285G>A c.1111G>A p.V371M
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
GDF9
Ovis aries
sheep - (species)
Published - Accepted by Curator
GDF9
Fertility (increased ovulation rate)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Hanrahan JP; Gregan SM; Mulsant P ; et al. (2004)
Mutations in the genes for oocyte-derived growth factors GDF9 and BMP15 are associated with both inc[...]
GP00002187
GDF9
O60383
Physiology
g.41841212C>T c.1184C>T p.S395F
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
GDF9
Ovis aries
sheep - (species)
Published - Accepted by Curator
GDF9
Fertility (increased ovulation rate)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Souza CJ; McNeilly AS; Benavides MV ; et al. (2014)
Mutation in the protease cleavage site of GDF9 increases ovulation rate and litter size in heterozyg[...]
GP00002188
GDF9
O60383
Physiology
g.41841453C>T c.943C>T p.R315C
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
GDF9
Ovis aries
sheep - (species)
Published - Accepted by Curator
GH
Body size (dwarfism)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
McCormack BL; Chase CC; Olson TA ; et al. (2009)
A miniature condition in Brahman cattle is associated with a single nucleotide mutation within the g[...]
GP00002037
GH1
P01241
Morphology
g.48768780C>T c.593C>T p.T198M
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
GH
Bos taurus
cattle - (species)
Published - Accepted by Curator
Ghd7
Flowering time
Inflorescence morphology
Unknown,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Xue W; Xing Y; Weng X ; et al. (2008)
Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice.
GP00000393
GHD7
E5RQA1
Physiology
Morphology
unknown
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Ghd7
Oryza sativa
rice - (species)
Published - Accepted by Curator
GIGANTEA
Photoperiod response
Circadian rhythm
Coding,
SNP
Brassica rapa
field mustard - (species)
Domesticated
Linkage Mapping
Xie Q; Lou P; Hermand V ; et al. (2015)
Allelic polymorphism of GIGANTEA is responsible for naturally occurring variation in circadian perio[...]
GP00000396
GI
Q9SQI2
Physiology
Physiology
Ser264Ala
Brassica rapa
field mustard - (species)
Brassica rapa
field mustard - (species)
GIGANTEA
Brassica rapa
field mustard - (species)
Published - Accepted by Curator
GL3.1
Grain size
2 Mutations:
Coding
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Qi P; Lin YS; Song XJ ; et al. (2012)
The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;[...]
GP00000397
GL3
Q9FN69
Morphology
2 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GL3.1
Oryza sativa
rice - (species)
Published - Accepted by Curator
GL7
Grain size
Grain quality
Gene Amplification,
Indel
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang Y; Xiong G; Hu J ; et al. (2015)
Copy number variation at the GL7 locus contributes to grain size diversity in rice.
GP00001541
LNG1
Q9LF24
Morphology
Physiology
tandem duplication of a 17.1 kb segment containing GL7. Both copies encode exactly the same polypeptide and exhibit similar transcript levels leading to upregulation
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GL7
Oryza sativa
rice - (species)
Published - Accepted by Curator
glutamate dehydrogenase (GDH)
Silk yield
Unknown,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Association Mapping
Xiang H; Liu X; Li M ; et al. (2018)
The evolutionary road from wild moth to domestic silkworm.
1 Additional References
GP00002406
bb8
Q9VCN3
Physiology
Increased expression in the domesticated strains
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
glutamate dehydrogenase (GDH)
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
glutamate synthase (GOGAT)
Silk yield
Unknown,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Association Mapping
Xiang H; Liu X; Li M ; et al. (2018)
The evolutionary road from wild moth to domestic silkworm.
1 Additional References
GP00002407
GS
M9NFH8
Physiology
Increased expression in the domesticated strains at the larval stage
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
glutamate synthase (GOGAT)
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
glutamine synthetase 2 (GS)
Silk yield
Unknown,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Association Mapping
Xiang H; Liu X; Li M ; et al. (2018)
The evolutionary road from wild moth to domestic silkworm.
1 Additional References
GP00002405
Gs2
P20478
Physiology
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
glutamine synthetase 2 (GS)
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
Glypican-3 (Gpc3)
Body size (weight)
Cis-regulatory,
Unknown
Mus musculus
house mouse - (species)
Domesticated
Linkage Mapping
Oliver F; Christians JK; Liu X ; et al. (2005)
Regulatory variation at glypican-3 underlies a major growth QTL in mice.
GP00000407
Gpc3
Q8CFZ4
Physiology
unknown; possible 3'UTR variation
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species)
Glypican-3 (Gpc3)
Mus musculus
house mouse - (species)
Published - Accepted by Curator
GmHs1-1 (Glyma02g43700.1)
Seed hardness
Seed coat permeability
Coding,
SNP
Glycine max
soybean - (species) D
Domesticated
Linkage Mapping
Sun L; Miao Z; Cai C ; et al. (2015)
GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean.
GP00001543
Hs1
I1JIK2
Physiology
Physiology
C>T p.Thr>Met predicted to affect the alpha-helix of the protein
Glycine soja
(species)
Glycine max
soybean - (species) D
GmHs1-1 (Glyma02g43700.1)
Glycine max
soybean - (species)
Published - Accepted by Curator
GPA1
Pheromone response
Cell elongation
Coding,
SNP
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Yvert G; Brem RB; Whittle J ; et al. (2003)
Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors.
1 Additional References
GP00000410
GPA1
P08539
Physiology
Physiology
Ser469Ile
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
GPA1
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
GPR133
Body size (weight)
Cis-regulatory,
Unknown
Mus musculus
house mouse - (species)
Domesticated
Association Mapping
Chan YF; Jones FC; McConnell E ; et al. (2012)
Parallel selection mapping using artificially selected mice reveals body weight control loci.
GP00000411
ADGRD1
Q6QNK2
Physiology
unknown
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species)
GPR133
Mus musculus
house mouse - (species)
Published - Accepted by Curator
GPR22
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Batcher K; Varney S; Affolter VK ; et al. (2022)
An SNN retrocopy insertion upstream of GPR22 is associated with dark red coat color in Poodles.
GP00002389
GPR22
Q99680
Morphology
A SNNL1 retrocopy element is inserted within the intron of COG5 and 2.8kbp upstream of and in the same orientation as GPR22. It is likely disrupting regulation of the CPR22 gene, resulting in higher gene expression and atypical expression in the skin.
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
GPR22
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
GRAIN INCOMPLETE FILLING 1
Grain weight
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang E; Wang J; Zhu X ; et al. (2008)
Control of rice grain-filling and yield by a gene with a potential signature of domestication.
GP00000413
CIN2
Q0JDC5
Morphology
unknown
Oryza rufipogon
(species)
Oryza sativa
rice - (species)
GRAIN INCOMPLETE FILLING 1
Oryza sativa
rice - (species)
Published - Accepted by Curator
GRAMD3
Coloration (skin)
Cis-regulatory,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Association Mapping
Xu J; Lin S; Gao X ; et al. (2017)
Mapping of Id locus for dermal shank melanin in a Chinese indigenous chicken breed.
GP00002391
GRAMD3
F1NDM3
Morphology
No coding mutation in GRAMD3. The expression of GRAMD3 gene in the dermis tissues of the shank was significantly (P = 0.010738 < 0.05) higher in 350-day-old Gushi chickens characterized by the dermal shank pigmentation than in one-day-old Gushi chickens. Variation in the flanking region of GRAMD3 probably leads to the abnormal expression of GRAMD3.
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
GRAMD3
Gallus gallus
chicken - (species)
Published - Accepted by Curator
grassy tillers1
Plant architecture (number of ears)
Cis-regulatory,
Unknown
Zea mays
(species)
Domesticated
Linkage Mapping
Wills DM; Whipple CJ; Takuno S ; et al. (2013)
From many, one: genetic control of prolificacy during maize domestication.
GP00000414
gt1
G1AQA5
Morphology
unknown but narrow 2.7kb interval
Zea mays
(species)
Zea mays
(species)
grassy tillers1
Zea mays
(species)
Published - Accepted by Curator
Growth Hormone Receptor
Milk yield
Coding,
SNP
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Viitala S; Szyda J; Blott S ; et al. (2006)
The role of the bovine growth hormone receptor and prolactin receptor genes in milk, fat and protein[...]
1 Additional References
GP00000416
Ghr
P16882
Physiology
Phe279Tyr
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
Growth Hormone Receptor
Bos taurus
cattle - (species)
Published - Accepted by Curator
growth hormone receptor (GHR)
Body size (weight)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Rimbault M; Beale HC; Schoenebeck JJ ; et al. (2013)
Derived variants at six genes explain nearly half of size reduction in dog breeds.
GP00001475
GHR
Q9TU69
Morphology
G>A in exon 5 p.E191K in extracellular domain
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
growth hormone receptor (GHR)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
growth hormone receptor (GHR)
Body size (weight)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Rimbault M; Beale HC; Schoenebeck JJ ; et al. (2013)
Derived variants at six genes explain nearly half of size reduction in dog breeds.
GP00001476
GHR
Q9TU69
Morphology
C>T in exon 5 p.P177L in extracellular domain
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
growth hormone receptor (GHR)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Growth Hormone Receptor (GHR)
Body size (dwarfism)
Coding,
Deletion
N
Gallus gallus
chicken - (species) D
Domesticated
Association Mapping
Agarwal SK; Cogburn LA; Burnside J (1994)
Dysfunctional growth hormone receptor in a strain of sex-linked dwarf chicken: evidence for a mutati[...]
GP00002189
GHR
P10912
Morphology
deletion of 1773 bp in the 3' end of the coding region N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Growth Hormone Receptor (GHR)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
GS3
Grain size
Coding,
SNP
N
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Fan C; Xing Y; Mao H ; et al. (2006)
GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, en[...]
1 Additional References
GP00000417
GS3
C6L686
Morphology
C55*;TGC>TGA causing a 178-aa truncation in the C-terminus of the predicted protein N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GS3
Oryza sativa
rice - (species)
Published - Accepted by Curator
GS5
Grain size
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Li Y; Fan C; Xing Y ; et al. (2011)
Natural variation in GS5 plays an important role in regulating grain size and yield in rice.
GP00000418
GS5
B8AYD6
Morphology
Promoter variation
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GS5
Oryza sativa
rice - (species)
Published - Accepted by Curator
GW2
Grain size
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Song XJ; Huang W; Shi M ; et al. (2007)
A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase.
GP00000424
GW2
A4GWX9
Morphology
1bp deletion resulting in a premature stop codon in exon 4; the premature stop codon led to truncation of 310 amino acid residues N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
GW2
Oryza sativa
rice - (species)
Published - Accepted by Curator
GW2
Grain size
Coding,
Insertion
N
Triticum aestivum
bread wheat - (species) D
Domesticated
Linkage Mapping
Yang Z; Bai Z; Li X ; et al. (2012)
SNP identification and allelic-specific PCR markers development for TaGW2, a gene linked to wheat ke[...]
GP00000425
GW2
A4GWX9
Morphology
1bp insertion resulting in premature stop codon N
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species) D
GW2
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
GW7
Grain shape
Grain quality
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang S; Li S; Liu Q ; et al. (2015)
The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and [...]
GP00001540
TON1A
Q9FQ25
Morphology
Physiology
18 SNPs and 9 indels observed in the promoter region and exon 1 and in particular an 11-bp deletion and 18-bp insertion near GTAC motifs which are normally binded by OsSPL16 repressor (reduced binding increasing transcription)
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
GW7
Oryza sativa
rice - (species)
Published - Accepted by Curator
HAO1
Fertility (egg production)
Bird head morphology (male comb)
Cis-regulatory,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Linkage Mapping
Johnsson M; Gustafson I; Rubin CJ ; et al. (2012)
A sexual ornament in chickens is affected by pleiotropic alleles at HAO1 and BMP2, selected during d[...]
1 Additional References
GP00000437
HAO1
E1BRR7
Physiology
Morphology
unknown; but intergenic QTL peak with decomposed effects on expression of BMP2 and HAO1
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
HAO1
Gallus gallus
chicken - (species)
Published - Accepted by Curator
HAS2
Wrinkled skin (Shar-Pei dogs)
Cis-regulatory,
Unknown
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Akey JM; Ruhe AL; Akey DT ; et al. (2010)
Tracking footprints of artificial selection in the dog genome.
GP00000438
HAS2
J9PB16
Morphology
unknown
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
HAS2
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Hd1
Flowering time
Coding,
Insertion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Doi K; Izawa T; Fuse T ; et al. (2004)
Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-[...]
GP00000439
HD1
Q9FDX8
Physiology
Retro-element-like inserted in exon 2 N
Oryza glaberrima
African rice - (species)
Oryza sativa
rice - (species) D
Hd1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Hd1
Flowering time
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Yano M; Katayose Y; Ashikari M ; et al. (2000)
Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Ara[...]
1 Additional References
GP00000441
HD1
Q9FDX8
Physiology
2bp deletion in the putative exon 2 N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Hd1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Hd1
Flowering time
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Takahashi Y; Teshima KM; Yokoi S ; et al. (2009)
Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of fl[...]
GP00001722
HD1
Q9FDX8
Physiology
1bp deletion at position 606 ; presumptive protein truncated N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Hd1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Hd1
Flowering time
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Takahashi Y; Teshima KM; Yokoi S ; et al. (2009)
Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of fl[...]
GP00001723
HD1
Q9FDX8
Physiology
1bp deletion at position 321 ; presumptive protein truncated N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Hd1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Hd1
Flowering time
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Takahashi Y; Teshima KM; Yokoi S ; et al. (2009)
Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of fl[...]
GP00001724
HD1
Q9FDX8
Physiology
4bp deletion at position 1089 ; presumptive protein truncated N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Hd1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Hd1
Flowering time
Coding,
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Takahashi Y; Teshima KM; Yokoi S ; et al. (2009)
Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of fl[...]
GP00001725
HD1
Q9FDX8
Physiology
C to T – stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Hd1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Hd6a
Flowering time
Coding,
SNP
N
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Takahashi Y; Shomura A; Sasaki T ; et al. (2001)
Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit [...]
GP00000442
HD6
Q9AR27
Physiology
K91*; AAG>TAG N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Hd6a
Oryza sativa
rice - (species)
Published - Accepted by Curator
HEADING DATE 1
Flowering time (latitudinal adaptation)
Cis-regulatory,
Insertion
N
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Domesticated
Candidate Gene
Goretti D; Martignago D; Landini M ; et al. (2017)
Transcriptional and Post-transcriptional Mechanisms Limit Heading Date 1 (Hd1) Function to Adapt Ric[...]
GP00001674
HD1
Q9FDX8
Physiology
Hd1(EH) allele with a 4.4 kb mobile element inserted at position -166pb that suppressed gene transcription N
Oryza sativa
rice - (species)
Oryza sativa Japonica Group
Japanese rice - (no rank) D
HEADING DATE 1
Oryza sativa Japonica Group
Japanese rice - (no rank)
Published - Accepted by Curator
Heading Date 1 (HD1)
Flowering time
Coding,
Deletion
N
Sorghum virgatum
(species) D
Domesticated
Association Mapping
Liu H; Liu H; Zhou L ; et al. (2015)
Parallel Domestication of the Heading Date 1 Gene in Cereals.
GP00001408
CO
Q39057
Physiology
5bp deletion in the coding sequence leading to gene frameshift N
Sorghum bicolor
sorghum - (species)
Sorghum virgatum
(species) D
Heading Date 1 (HD1)
Sorghum virgatum
(species)
Published - Accepted by Curator
Heading Date 1 (HD1)
Flowering time
Coding,
SNP
N
Setaria italica
foxtail millet - (species) D
Domesticated
Association Mapping
Liu H; Liu H; Zhou L ; et al. (2015)
Parallel Domestication of the Heading Date 1 Gene in Cereals.
GP00001410
CO
Q39057
Physiology
splicing variant at position 787 GT>AT resulting in a splicing shift to position 754 introducing a deletion of 33 bp in the transcript and 11 aa in the protein N
Setaria italica
foxtail millet - (species)
Setaria italica
foxtail millet - (species) D
Heading Date 1 (HD1)
Setaria italica
foxtail millet - (species)
Published - Accepted by Curator
heavy metal atpase3 (HMA3)
Metal tolerance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Ueno D; Yamaji N; Kono I ; et al. (2010)
Gene limiting cadmium accumulation in rice.
GP00000445
HMA3
P0CW78
Physiology
H80R
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
heavy metal atpase3 (HMA3)
Oryza sativa
rice - (species)
Published - Accepted by Curator
HES7
Organ size (tail; short)
Coding,
SNP
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Lyons LA; Creighton EK; Alhaddad H ; et al. (2016)
Whole genome sequencing in cats, identifies new models for blindness in AIPL1 and somite segmentatio[...]
1 Additional References
GP00002190
HES7
Q9BYE0
Morphology
g.2819475A>G c.5A>G p.V2A
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
HES7
Felis catus
domestic cat - (species)
Published - Accepted by Curator
HM1 = HC toxin reductase (HCTR)
Pathogen resistance
Unknown,
Unknown
Zea mays
(species)
Domesticated
Candidate Gene
Multani DS; Meeley RB; Paterson AH ; et al. (1998)
Plant-pathogen microevolution: molecular basis for the origin of a fungal disease in maize.
GP00000480
hm1
O49163
Physiology
Not identified
Zea mays
(species)
Zea mays
(species)
HM1 = HC toxin reductase (HCTR)
Zea mays
(species)
Published - Accepted by Curator
HM1 = HC toxin reductase (HCTR) [possible pseudo-replicate from other Maize entry]
Pathogen resistance
Coding,
Insertion
N
Zea mays
(species) D
Domesticated
Linkage Mapping
Johal GS; Briggs SP (1992)
Reductase activity encoded by the HM1 disease resistance gene in maize.
1 Additional References
GP00000481
hm1
O49163
Physiology
256-bp transposable element insertion in exon 4 N
Zea mays
(species)
Zea mays
(species) D
HM1 = HC toxin reductase (HCTR) [possible pseudo-replicate from other Maize entry]
Zea mays
(species)
Published - Accepted by Curator
HM2 = HC toxin reductase (HCTR)
Pathogen resistance
Coding,
Deletion
N
Zea mays
(species) D
Domesticated
Candidate Gene
Chintamanani S; Multani DS; Ruess H ; et al. (2008)
Distinct mechanisms govern the dosage-dependent and developmentally regulated resistance conferred b[...]
GP00000482
hm2
B8QWA3
Physiology
deletion from exon 2 (nucleotide 420) to beyond the confines of the hm2 gene into an unknown genomic region. N
Zea mays
(species)
Zea mays
(species) D
HM2 = HC toxin reductase (HCTR)
Zea mays
(species)
Published - Accepted by Curator
HM2 = HC toxin reductase (HCTR)
Pathogen resistance
Coding,
Insertion
N
Zea mays
(species) D
Domesticated
Candidate Gene
Chintamanani S; Multani DS; Ruess H ; et al. (2008)
Distinct mechanisms govern the dosage-dependent and developmentally regulated resistance conferred b[...]
GP00000483
hm2
B8QWA3
Physiology
8-bp insertion in exon 1 that disrupt the reading frame and introduces a stop codon shortly after the beginning of the gene N
Zea mays
(species)
Zea mays
(species) D
HM2 = HC toxin reductase (HCTR)
Zea mays
(species)
Published - Accepted by Curator
HMGA2
Body size
Unknown,
Unknown
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Akey JM; Ruhe AL; Akey DT ; et al. (2010)
Tracking footprints of artificial selection in the dog genome.
1 Additional References
GP00000484
HMGA2
P52926
Morphology
unknown
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
HMGA2
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
HMGA2
Body size
Unknown,
Unknown
Equus caballus
horse - (species)
Domesticated
Association Mapping
Makvandi-Nejad S; Hoffman GE; Allen JJ ; et al. (2012)
Four loci explain 83% of size variation in the horse.
GP00000485
HMGA2
P52926
Morphology
unknown
Equus caballus
horse - (species)
Equus caballus
horse - (species)
HMGA2
Equus caballus
horse - (species)
Published - Accepted by Curator
HMGA2
Ear size
Unknown,
Unknown
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Li P; Xiao S; Wei N ; et al. (2012)
Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group[...]
GP00000487
HMGA2
P52926
Morphology
unknown
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
HMGA2
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
HMGA2
Body size (dwarfism)
Cranio-facial morphology
Coding,
Deletion
N
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Association Mapping
Carneiro M; Hu D; Archer J ; et al. (2017)
Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA[...]
GP00001675
HMGA2
P52926
Morphology
Morphology
deletion of 12.1 kb overlapping the promoter region and first three exons leading to inactivation of the gene. The 5'-end of this deletion overlaps a CSINE2 element N
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
HMGA2
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
HMX1
Organ size (ear; cropped)
Cis-regulatory,
Insertion
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Koch CT; Bruggmann R; Tetens J ; et al. (2013)
A non-coding genomic duplication at the HMX1 locus is associated with crop ears in highland cattle.
GP00002191
HMX1
Q9NP08
Morphology
76bp duplication in an ultra-conserved enhancer located 148 kb apart of the coding region of HMX1
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
HMX1
Bos taurus
cattle - (species)
Published - Accepted by Curator
Hooded
Flower morphology
Cis-regulatory,
Insertion
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Müller KJ; Romano N; Gerstner O ; et al. (1995)
The barley Hooded mutation caused by a duplication in a homeobox gene intron.
GP00000488
KNOX3
Q43484
Morphology
305bp duplication in intron 4
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
Hooded
Hordeum vulgare
(species)
Published - Accepted by Curator
Hoxb8
Feather (bird face)
Cis-regulatory,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Guo Y; Gu X; Sheng Z ; et al. (2016)
A Complex Structural Variation on Chromosome 27 Leads to the Ectopic Expression of HOXB8 and the Muf[...]
GP00002193
Hoxb8
P09632
Morphology
Complex Structural Variation with 3 CNVs including a 14.8kb copy of hoxb7 + hoxb8 ; results in ectopic (unrepressed) expression of hoxb8 in feathers especially in the facial region
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Hoxb8
Gallus gallus
chicken - (species)
Published - Accepted by Curator
HOXC8 - uncertain
Feathers (crest morphology)
Cis-regulatory,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Association Mapping
Wang Y; Gao Y; Imsland F ; et al. (2012)
The crest phenotype in chicken is associated with ectopic expression of HOXC8 in cranial skin.
GP00000489
HOXC8
Q9YH13
Morphology
unknown
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
HOXC8 - uncertain
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Hs1 = pro-1
Pathogen resistance (parasite, nematodes) (nematodes)
Gene Loss,
Complex Change
N
Beta vulgaris
(species)
Domesticated
Linkage Mapping
Cai D; Kleine M; Kifle S ; et al. (1997)
Positional cloning of a gene for nematode resistance in sugar beet.
GP00000490
HSPRO1
Q9LY61
Physiology
cDNA sequence lacking in genomic DNA N
Patellifolia
(genus)
Beta vulgaris
(species)
Hs1 = pro-1
Beta vulgaris
(species)
Published - Accepted by Curator
HTR2C serotonin receptor
Immune response (complement activation)
Unknown,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Association Mapping
Biscarini F; Bovenhuis H; van Arendonk JA ; et al. (2010)
Across-line SNP association study of innate and adaptive immune response in laying hens.
GP00001595
HTR2C
F1N989
Physiology
unknown
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
HTR2C serotonin receptor
Gallus gallus
chicken - (species)
Published - Accepted by Curator
HTR3A serotonin receptor
Immune response (antibody titre)
Unknown,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Association Mapping
Biscarini F; Bovenhuis H; van Arendonk JA ; et al. (2010)
Across-line SNP association study of innate and adaptive immune response in laying hens.
GP00001596
HTR3A
A0A1D5P8L2
Physiology
unknown
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
HTR3A serotonin receptor
Gallus gallus
chicken - (species)
Published - Accepted by Curator
HvbHLH1
Coloration
Coding,
Deletion
N
Hordeum vulgare
(species) D
Domesticated
Association Mapping
Cockram J; White J; Zuluaga DL ; et al. (2010)
Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genom[...]
GP00000493
bHLH1
E5FCX3
Morphology
16bp deletion resulting in premature stop codon N
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
HvbHLH1
Hordeum vulgare
(species)
Published - Accepted by Curator
I cluster
Pathogen resistance
Unknown,
Unknown
Phaseolus vulgaris
(species) D
Domesticated
Linkage Mapping
Vallejos CE; Astua-Monge G; Jones V ; et al. (2006)
Genetic and molecular characterization of the I locus of Phaseolus vulgaris.
GP00000496
U5YMY7
Physiology
unknown; maps to a cluster of R-proteins
Phaseolus vulgaris
(species)
Phaseolus vulgaris
(species) D
I cluster
Phaseolus vulgaris
(species)
Published - Accepted by Curator
IGF2BP1
Body size (weight)
Cis-regulatory,
Unknown
Anas platyrhynchos
mallard - (species) D
Domesticated
Linkage Mapping
Zhou Z; Li M; Cheng H ; et al. (2018)
An intercross population study reveals genes associated with body size and plumage color in ducks.
GP00002128
IGF2BP1
O42254
Morphology
We found that the phenotypic values of body size related traits together with IGF2BP1 expression levels were successfully fine-mapped of the causal variation in an ~100-kb region (chr28: 4,413,785-4,513,671) located on the 148 kb upstream of the IGF2BP1 gene
Anas platyrhynchos
mallard - (species)
Anas platyrhynchos
mallard - (species) D
IGF2BP1
Anas platyrhynchos
mallard - (species)
Published - Accepted by Curator
Indian hedgehog (IHH)
Limb size (legs)
Gene Loss,
Deletion
N
Gallus gallus
chicken - (species) D
Domesticated
Association Mapping
Jin S; Zhu F; Wang Y ; et al. (2016)
Deletion of Indian hedgehog gene causes dominant semi-lethal Creeper trait in chicken.
GP00002194
IHH
Q98938
Morphology
11,896 bp large deletion region (chr7: 21,798,705-21,810,600) covering the entire Indian hedgehog (IHH) gene N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Indian hedgehog (IHH)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Insulin-like growth factor 1 (IGF1)
Body size
Cis-regulatory,
Unknown
Canis lupus familiaris
dog - (subspecies)
Domesticated
Association Mapping
Sutter NB; Bustamante CD; Chase K ; et al. (2007)
A single IGF1 allele is a major determinant of small size in dogs.
1 Additional References
GP00000501
Igf1
P05017
Morphology
Not identified / several haplotypes
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies)
Insulin-like growth factor 1 (IGF1)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Insulin-like growth factor 2 (IGF2)
Muscular mass
Fat deposition
Heart size
Cis-regulatory,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Van Laere AS; Nguyen M; Braunschweig M ; et al. (2003)
A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig.
GP00000502
Igf2
P09535
Morphology
Physiology
Morphology
1bp change
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
Insulin-like growth factor 2 (IGF2)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Insulin-like growth factor receptor 1 (IGF1R)
Body size (weight)
Coding,
SNP
Homo sapiens
human - (species) D
Domesticated
Candidate Gene
Rimbault M; Beale HC; Schoenebeck JJ ; et al. (2013)
Derived variants at six genes explain nearly half of size reduction in dog breeds.
GP00001479
IGF1R
P08069
Morphology
G>A p.R204H in exon 2
Canis lupus
gray wolf - (species)
Homo sapiens
human - (species) D
Insulin-like growth factor receptor 1 (IGF1R)
Homo sapiens
human - (species)
Published - Accepted by Curator
Interleukin 10 (IL10)
Immune response (antibody titre and complement activation)
Unknown,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Association Mapping
Biscarini F; Bovenhuis H; van Arendonk JA ; et al. (2010)
Across-line SNP association study of innate and adaptive immune response in laying hens.
GP00001597
IL10
Q6A2H4
Physiology
unknown
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
Interleukin 10 (IL10)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Interleukin 12B (IL12B)
Immune response (antibody titre)
Unknown,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Association Mapping
Biscarini F; Bovenhuis H; van Arendonk JA ; et al. (2010)
Across-line SNP association study of innate and adaptive immune response in laying hens.
GP00001594
IL-12B
Q6X0K9
Physiology
unknown
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
Interleukin 12B (IL12B)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Interleukin 17A (IL17A)
Immune response (antibody titre and complement activation)
Unknown,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Association Mapping
Biscarini F; Bovenhuis H; van Arendonk JA ; et al. (2010)
Across-line SNP association study of innate and adaptive immune response in laying hens.
GP00001593
IL17A
B4ER12
Physiology
unknown
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
Interleukin 17A (IL17A)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
IRA2
Growth rate (environment-dependent)
Coding,
Unknown
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Smith EN; Kruglyak L (2008)
Gene-environment interaction in yeast gene expression.
GP00000505
IRA2
P19158
Physiology
unknown
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
IRA2
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
IRF2BP2
Hair type (woolly)
Cis-regulatory,
Insertion
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Demars J; Cano M; Drouilhet L ; et al. (2017)
Genome-Wide Identification of the Mutation Underlying Fleece Variation and Discriminating Ancestral [...]
GP00002195
IRF2BP2
Q7Z5L9
Morphology
insertion of an antisense EIF2S2 retrogene (asEIF2S2) into the 3′ UTR of the IRF2BP2 gene ; RNA-RNA hybrid creates a long endogenous double-stranded RNA which alters the expression of both EIF2S2 and IRF2BP2 mRNA
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
IRF2BP2
Ovis aries
sheep - (species)
Published - Accepted by Curator
Kit
Coloration (coat ; white-spotting)
Coding,
Insertion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Wong AK; Ruhe AL; Robertson KR ; et al. (2013)
A de novo mutation in KIT causes white spotting in a subpopulation of German Shepherd dogs.
GP00002228
Kit
P05532
Morphology
a 1-bp insertion of an adenine 70 bases downstream of the beginning of exon 2 resulting in frameshift N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Kit
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Gene Amplification,
Complex Change
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Durkin K; Coppieters W; Drögemüller C ; et al. (2012)
Serial translocation by means of circular intermediates underlies colour sidedness in cattle.
GP00000514
Kit
P05532
Morphology
Copy Number Variation of <600kb segments encompassing KIT
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
Kit (type III receptor protein-tyrosine kinase)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Linkage Mapping
Brooks SA; Bailey E (2005)
Exon skipping in the KIT gene causes a Sabino spotting pattern in horses.
GP00000515
Kit
P05532
Morphology
T->A in intron 16; leads to skipping of exon 17
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
N
Equus caballus
horse - (species) D
Domesticated
Linkage Mapping
Haase B; Brooks SA; Schlumbaum A ; et al. (2007)
Allelic heterogeneity at the equine KIT locus in dominant white (W) horses.
GP00000516
Kit
P05532
Morphology
c.2151C>G pY717* N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Insertion
Felis catus
domestic cat - (species) D
Domesticated
Association Mapping
David VA; Menotti-Raymond M; Wallace AC ; et al. (2014)
Endogenous retrovirus insertion in the KIT oncogene determines white and white spotting in domestic [...]
GP00000517
Kit
P05532
Morphology
full-length (7125 bp) FERV1 endogenous retrovirus insertion in intron
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
Kit (type III receptor protein-tyrosine kinase)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Indel
Felis catus
domestic cat - (species) D
Domesticated
Association Mapping
Montague MJ; Li G; Gandolfi B ; et al. (2014)
Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology[...]
GP00000518
Kit
P05532
Morphology
Two nucleotide changes affecting site 3 of codon 345 and site 1 of codon 346 - resulting in Glu345Asp + His346Asn
c. 1035_1036delinsCA GAGCAY > GACAAY
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
Kit (type III receptor protein-tyrosine kinase)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Deletion
Felis catus
domestic cat - (species) D
Domesticated
Association Mapping
David VA; Menotti-Raymond M; Wallace AC ; et al. (2014)
Endogenous retrovirus insertion in the KIT oncogene determines white and white spotting in domestic [...]
GP00000519
Kit
P05532
Morphology
Excision of the full-length FERV1 elevement leaving the two LTR residues
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
Kit (type III receptor protein-tyrosine kinase)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
2 Mutations:
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Linkage Mapping
Marklund S; Kijas J; Rodriguez-Martinez H ; et al. (1998)
Molecular basis for the dominant white phenotype in the domestic pig.
3 Additional References
GP00000520
Kit
P05532
Morphology
2 mutations
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
Kit (type III receptor protein-tyrosine kinase)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Deletion
Vulpes vulpes
red fox - (species) D
Domesticated
Linkage Mapping
Johnson JL; Kozysa A; Kharlamova AV ; et al. (2015)
Platinum coat color in red fox (Vulpes vulpes) is caused by a mutation in an autosomal copy of KIT.
GP00000521
Kit
P05532
Morphology
splice mutation; G to A substitution in the first nucleotide of intron 17; leads to skipping of exon 17.
Vulpes vulpes
red fox - (species)
Vulpes vulpes
red fox - (species) D
Kit (type III receptor protein-tyrosine kinase)
Vulpes vulpes
red fox - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Insertion
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Candidate Gene
Rubin CJ; Megens HJ; Martinez Barrio A ; et al. (2012)
Strong signatures of selection in the domestic pig genome.
1 Additional References
GP00001326
Kit
P05532
Morphology
4.3kb duplication (DUP2) located about 100 kb upstream of KIT
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
Kit (type III receptor protein-tyrosine kinase)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Unknown,
Unknown
Vulpes vulpes
red fox - (species) D
Domesticated
Association Mapping
Kukekova AV; Johnson JL; Kharlamova AV ; et al. (2016)
Georgian white coat color of red fox (Vulpes vulpes) maps to fox chromosome 2 in the region containi[...]
GP00001328
Kit
P05532
Morphology
unknown
Vulpes vulpes
red fox - (species)
Vulpes vulpes
red fox - (species) D
Kit (type III receptor protein-tyrosine kinase)
Vulpes vulpes
red fox - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (skin; coat)
Coding,
SNP
Equus asinus
ass - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Leeb T (2015)
Two variants in the KIT gene as candidate causative mutations for a dominant white and a white spott[...]
GP00001340
Kit
P05532
Morphology
c.662A>C p.Tyr221Ser
Equus asinus
ass - (species)
Equus asinus
ass - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus asinus
ass - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (skin; coat)
Coding,
SNP
Equus asinus
ass - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Leeb T (2015)
Two variants in the KIT gene as candidate causative mutations for a dominant white and a white spott[...]
GP00001341
Kit
P05532
Morphology
c.1978+2T>A in splice donor site
Equus asinus
ass - (species)
Equus asinus
ass - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus asinus
ass - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00001344
Kit
P05532
Morphology
c.1789G>A p.G597R
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Gene Amplification,
Complex Change
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Brenig B; Beck J; Floren C ; et al. (2013)
Molecular genetics of coat colour variations in White Galloway and White Park cattle.
GP00001345
Kit
P05532
Morphology
duplication and aberrant insertion on chromosome 29
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Kit (type III receptor protein-tyrosine kinase)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Other,
SNP
Vulpes lagopus
Arctic fox - (species) D
Domesticated
Candidate Gene
Yan SQ; Hou JN; Bai CY ; et al. (2014)
A base substitution in the donor site of intron 12 of KIT gene is responsible for the dominant white[...]
GP00002192
Kit
P05532
Morphology
dominant white coat colour of blue fox results from an exon 12 skipping caused by a c.1867+1G>T substitution in the first nucleotide of intron 12 of the KIT gene
Vulpes lagopus
Arctic fox - (species)
Vulpes lagopus
Arctic fox - (species) D
Kit (type III receptor protein-tyrosine kinase)
Vulpes lagopus
Arctic fox - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Insertion
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Candidate Gene
Rubin CJ; Megens HJ; Martinez Barrio A ; et al. (2012)
Strong signatures of selection in the domestic pig genome.
1 Additional References
GP00002196
Kit
P05532
Morphology
the patch allele comprises a 450kb duplication that includes KIT (roughly in the middle)
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
Kit (type III receptor protein-tyrosine kinase)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Gene Amplification,
Complex Change
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Küttel L; Letko A; Häfliger IM ; et al. (2019)
A complex structural variant at the KIT locus in cattle with the Pinzgauer spotting pattern.
1 Additional References
GP00002197
Kit
P05532
Morphology
Complex chromosomal rearragements including a ~310-kb duplication
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Kit (type III receptor protein-tyrosine kinase)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Schlumbaum A ; et al. (2007)
Allelic heterogeneity at the equine KIT locus in dominant white (W) horses.
GP00002198
Kit
P05532
Morphology
c.706A>T p.K236* N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Schlumbaum A ; et al. (2007)
Allelic heterogeneity at the equine KIT locus in dominant white (W) horses.
GP00002199
Kit
P05532
Morphology
c.1805C>T p.A602V
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Schlumbaum A ; et al. (2007)
Allelic heterogeneity at the equine KIT locus in dominant white (W) horses.
GP00002200
Kit
P05532
Morphology
c.1960G>A p.G654R
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00002201
Kit
P05532
Morphology
c.2222-1G>A (putative splicing site)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00002202
Kit
P05532
Morphology
c.1126_1129delGAAC p.E376FfsX3 N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00002203
Kit
P05532
Morphology
c.2684+1G>A (putative splicing site)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00002204
Kit
P05532
Morphology
c.338-1G>C (putative splicing site)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00002205
Kit
P05532
Morphology
c.2193delG p.T732QfsX9 N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Brooks SA; Tozaki T ; et al. (2009)
Seven novel KIT mutations in horses with white coat colour phenotypes.
GP00002206
Kit
P05532
Morphology
c.856G>A p.G286R
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Tozaki T ; et al. (2011)
Five novel KIT mutations in horses with white coat colour phenotypes.
GP00002207
Kit
P05532
Morphology
c.1597T>C p.C533R
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Tozaki T ; et al. (2011)
Five novel KIT mutations in horses with white coat colour phenotypes.
GP00002208
Kit
P05532
Morphology
c.2021T>C p.L674P
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Tozaki T ; et al. (2011)
Five novel KIT mutations in horses with white coat colour phenotypes.
GP00002209
Kit
P05532
Morphology
c.2001A>T p.E667D
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Tozaki T ; et al. (2011)
Five novel KIT mutations in horses with white coat colour phenotypes.
GP00002210
Kit
P05532
Morphology
c.2472+5G>C (putative splicing mutation)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Tozaki T ; et al. (2011)
Five novel KIT mutations in horses with white coat colour phenotypes.
GP00002211
Kit
P05532
Morphology
c.2489A>T p.K830I
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Rieder S; Tozaki T ; et al. (2011)
Five novel KIT mutations in horses with white coat colour phenotypes.
GP00002212
Kit
P05532
Morphology
c.2392_2445del p.H798_N815del N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Jude R; Haase B ; et al. (2013)
Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes.
GP00002213
Kit
P05532
Morphology
c.2045G>A p.R682H
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Jude R; Haase B ; et al. (2013)
Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes.
GP00002214
Kit
P05532
Morphology
c.1322A>G p.Y441C
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Jude R; Haase B ; et al. (2013)
Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes.
GP00002215
Kit
P05532
Morphology
c.1346 + 1G>A (putative splicing mutation)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Haase B; Jagannathan V; Rieder S ; et al. (2015)
A novel KIT variant in an Icelandic horse with white-spotted coat colour.
GP00002216
Kit
P05532
Morphology
c.2369delC p.Ala790Glufs*20 N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Holl HM; Brooks SA; Carpenter ML ; et al. (2017)
A novel splice mutation within equine KIT and the W15 allele in the homozygous state lead to all whi[...]
GP00002217
Kit
P05532
Morphology
c.756+1G>C (putative splicing mutation)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Deletion
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Capomaccio S; Milanesi M; Nocelli C ; et al. (2017)
Splicing site disruption in the KIT gene as strong candidate for white dominant phenotype in an Ital[...]
GP00002218
Kit
P05532
Morphology
g.77736559C>T (putative splicing mutation)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Dürig N; Jude R; Holl H ; et al. (2017)
Whole genome sequencing reveals a novel deletion variant in the KIT gene in horses with white spotte[...]
GP00002219
Kit
P05532
Morphology
g.77;740;239_77;742;136del1898insTATAT ~1.9-kb deletion N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hoban R; Castle K; Hamilton N ; et al. (2018)
Novel KIT variants for dominant white in the Australian horse population.
GP00002220
Kit
P05532
Morphology
c.1473T>G p.Cys491Trp
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hoban R; Castle K; Hamilton N ; et al. (2018)
Novel KIT variants for dominant white in the Australian horse population.
GP00002221
Kit
P05532
Morphology
c.2536delA p.Ser846Valfs*15
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hoban R; Castle K; Hamilton N ; et al. (2018)
Novel KIT variants for dominant white in the Australian horse population.
GP00002222
Kit
P05532
Morphology
c.668T>C p.Leu223Pro
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hug P; Jude R; Henkel J ; et al. (2019)
A novel KIT deletion variant in a German Riding Pony with white-spotting coat colour phenotype.
GP00002223
Kit
P05532
Morphology
g.79;579;925-79;581;197del 1273bp deletion N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Kit (type III receptor protein-tyrosine kinase)
Equus caballus
horse - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat)
Cis-regulatory,
Deletion
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Linkage Mapping
Lim HT; Zhong T; Cho IC ; et al. (2011)
Novel alternative splicing by exon skipping in KIT associated with whole-body roan in an intercrosse[...]
1 Additional References
GP00002227
Kit
P05532
Morphology
U(26) repeat in intron 5 of the KIT gene with a single G interruption likely to mediate skipping of exon 5 of the gene in some tissues including skin ; the WT allele has an U(27) repeat interrupted by 5 G
Sus scrofa domesticus
domestic pig - (subspecies)
Sus scrofa domesticus
domestic pig - (subspecies) D
Kit (type III receptor protein-tyrosine kinase)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase)
Coloration (coat ; white-spotting)
Coding,
Deletion
N
Camelus dromedarius
Arabian camel - (species) D
Domesticated
Candidate Gene
Holl H; Isaza R; Mohamoud Y ; et al. (2017)
A Frameshift Mutation in KIT is Associated with White Spotting in the Arabian Camel.
GP00002229
Kit
P05532
Morphology
c.1842delG p.M614IfsX5 N
Camelus dromedarius
Arabian camel - (species)
Camelus dromedarius
Arabian camel - (species) D
Kit (type III receptor protein-tyrosine kinase)
Camelus dromedarius
Arabian camel - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase) [pseudoreplicate with two Bos taurus KIT entries]
Coloration (coat)
Gene Amplification,
Complex Change
Bos grunniens
domestic yak - (species) D
Domesticated
Candidate Gene
Zhang MQ; Xu X; Luo SJ (2014)
The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens).
GP00001342
Kit
P05532
Morphology
serial translocations Cs6 and Cs29
Bos grunniens
domestic yak - (species)
Bos grunniens
domestic yak - (species) D
Kit (type III receptor protein-tyrosine kinase) [pseudoreplicate with two Bos taurus KIT entries]
Bos grunniens
domestic yak - (species)
Published - Accepted by Curator
Kit (type III receptor protein-tyrosine kinase) [pseudoreplicate with two Bos taurus KIT entries]
Coloration (coat)
Unknown,
Complex Change
Bos grunniens
domestic yak - (species) D
Domesticated
Candidate Gene
Zhang MQ; Xu X; Luo SJ (2014)
The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens).
GP00001343
Kit
P05532
Morphology
haplotype Swf (indels and SNP)
Bos grunniens
domestic yak - (species)
Bos grunniens
domestic yak - (species) D
Kit (type III receptor protein-tyrosine kinase) [pseudoreplicate with two Bos taurus KIT entries]
Bos grunniens
domestic yak - (species)
Published - Accepted by Curator
Kit ligand
Coloration (coat)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Seitz JJ; Schmutz SM; Thue TD ; et al. (1999)
A missense mutation in the bovine MGF gene is associated with the roan phenotype in Belgian Blue and[...]
1 Additional References
GP00000101
KITLG
P21583
Morphology
Ala193Asp ; missense mutation at position 654 - according to OMIA: c.572C>A p.A191N N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Kit ligand
Bos taurus
cattle - (species)
Published - Accepted by Curator
KRT25
Hair type (curly)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Morgenthaler C; Diribarne M; Capitan A ; et al. (2017)
A missense variant in the coil1A domain of the keratin 25 gene is associated with the dominant curly[...]
1 Additional References
GP00002230
Krt25
Q8VCW2
Morphology
c.266G>A p.Arg89His
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
KRT25
Equus caballus
horse - (species)
Published - Accepted by Curator
KRT25
Hair type (curly)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Thomer A; Gottschalk M; Christmann A ; et al. (2018)
An epistatic effect of KRT25 on SP6 is involved in curly coat in horses.
GP00002288
Sp6
Q9ESX2
Morphology
c.1090G>A p.Asp364Asn
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
KRT25
Equus caballus
horse - (species)
Published - Accepted by Curator
KRT27
Hair type (curly)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Daetwyler HD; Capitan A; Pausch H ; et al. (2014)
Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle.
GP00002026
KRT27
Q0P5J6
Morphology
g.41636961C>G c.276C>G p.Asn92Lys
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
KRT27
Bos taurus
cattle - (species)
Published - Accepted by Curator
KRT6A
Feathers
Coding,
Deletion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Ng CS; Wu P; Foley J ; et al. (2012)
The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis.
GP00000527
Krt6a
P50446
Morphology
69bp deletion partially overlapping with exon 5
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
KRT6A
Gallus gallus
chicken - (species)
Published - Accepted by Curator
KRT71
Hair type (curly)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Cadieu E; Neff MW; Quignon P ; et al. (2009)
Coat variation in the domestic dog is governed by variants in three genes.
GP00000524
Krt71
Q9R0H5
Morphology
c.451A>T in exon 2 - Arg151Trp
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
KRT71
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
KRT71
Hair type (curly and hairless)
2 Mutations:
Coding
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Gandolfi B; Outerbridge CA; Beresford LG ; et al. (2010)
The naked truth: Sphynx and Devon Rex cat breed mutations in KRT71.
GP00000525
Krt71
Q9R0H5
Morphology
2 mutations
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
KRT71
Felis catus
domestic cat - (species)
Published - Accepted by Curator
KRT71
Hair type (curly and hairless)
Coding,
Deletion
N
Rattus norvegicus
Norway rat - (species) D
Domesticated
Linkage Mapping
Kuramoto T; Hirano R; Kuwamura M ; et al. (2010)
Identification of the rat Rex mutation as a 7-bp deletion at splicing acceptor site of the Krt71 gen[...]
GP00001729
Krt71
Q9R0H5
Morphology
a 7-bp deletion at the splicing acceptor site of intron 1. The deletion provoked a 6-amino acid in-frame deletion (p.Val149_Gln154del) in the alpha-helical rod domain of KRT71 protein N
Rattus norvegicus
Norway rat - (species)
Rattus norvegicus
Norway rat - (species) D
KRT71
Rattus norvegicus
Norway rat - (species)
Published - Accepted by Curator
KRT71
Hair type (curly and hairless)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Gandolfi B; Outerbridge CA; Beresford LG ; et al. (2010)
The naked truth: Sphynx and Devon Rex cat breed mutations in KRT71.
GP00001730
Krt71
Q9R0H5
Morphology
eight base pair deletion mutation in exon one of the keratin 71 (KRT71) c.334delTGTGCCCA p.Met93AsnfsX14 N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
KRT71
Bos taurus
cattle - (species)
Published - Accepted by Curator
KRT71
Hair type (curly)
Coding,
Indel
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Bauer A; Hadji Rasouliha S; Brunner MT ; et al. (2019)
A second KRT71 allele in curly coated dogs.
1 Additional References
GP00002231
Krt71
Q9R0H5
Morphology
c.1266_1273delinsACA p.Ser422ArgfsTer?
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
KRT71
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
KRT71
Hair type (curly)
Coding,
SNP
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Gandolfi B; Alhaddad H; Joslin SE ; et al. (2013)
A splice variant in KRT71 is associated with curly coat phenotype of Selkirk Rex cats.
GP00002232
Krt71
Q9R0H5
Morphology
c.445-1G>C in splice site likely disrupts the highly conserved acceptor splicing site of intron one. Sequence of the complete RNA transcript revealed that an alternative downstream acceptor was employed N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
KRT71
Felis catus
domestic cat - (species)
Published - Accepted by Curator
KRT75L4
Feathers
Coding,
Deletion
Gallus gallus
chicken - (species) D
Domesticated
Association Mapping
Guo X; Li YQ; Wang MS ; et al. (2018)
A parallel mechanism underlying frizzle in domestic chickens.
GP00002334
KRT75L4
A0A1L1RKR4
Morphology
15bp deletion resulting in loss of 5 conserved amino-acids
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
KRT75L4
Gallus gallus
chicken - (species)
Published - Accepted by Curator
LCORL
Body size
Unknown,
Unknown
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Lindholm-Perry AK; Sexten AK; Kuehn LA ; et al. (2011)
Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 [...]
GP00000535
LCORL
Q8N3X6
Morphology
Not identified
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
LCORL
Bos taurus
cattle - (species)
Published - Accepted by Curator
LCORL
Body size
Unknown,
Unknown
Equus caballus
horse - (species)
Domesticated
Linkage Mapping
Makvandi-Nejad S; Hoffman GE; Allen JJ ; et al. (2012)
Four loci explain 83% of size variation in the horse.
3 Additional References
GP00000536
LCORL
Q8N3X6
Morphology
Not identified
Equus caballus
horse - (species)
Equus caballus
horse - (species)
LCORL
Equus caballus
horse - (species)
Published - Accepted by Curator
LeSPL-CNR
Fruit ripening
Cis-regulatory,
Epigenetic Change
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Manning K; Tör M; Poole M ; et al. (2006)
A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibit[...]
GP00000539
101256245
Q0PY35
Physiology
Stable methylation in a 286bp region of the promoter
Solanum cheesmaniae
(species)
Solanum lycopersicum
tomato - (species) D
LeSPL-CNR
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
LEU2
Xenobiotic resistance
Gene Loss,
Complex Change
N
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Perlstein EO; Ruderfer DM; Roberts DC ; et al. (2007)
Genetic basis of individual differences in the response to small-molecule drugs in yeast.
GP00000542
LEU2
P04173
Physiology
Deletion N
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
LEU2
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
LIPH
Hair length
Coding,
Deletion
N
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Linkage Mapping
Diribarne M; Mata X; Chantry-Darmon C ; et al. (2011)
A deletion in exon 9 of the LIPH gene is responsible for the rex hair coat phenotype in rabbits (Ory[...]
GP00000550
Liph
Q8CIV3
Morphology
1bp deletion resulting in frameshift N
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
LIPH
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
Low-density lipoprotein receptor-related protein 2
Organ size (eye; enlarged)
3 Mutations:
Coding
N
Carassius auratus
goldfish - (species) D
Domesticated
Association Mapping
Kon T; Omori Y; Fukuta K ; et al. (2020)
The Genetic Basis of Morphological Diversity in Domesticated Goldfish.
GP00002349
LRP2
P98164
Morphology
3 mutations
Carassius auratus
goldfish - (species)
Carassius auratus
goldfish - (species) D
Low-density lipoprotein receptor-related protein 2
Carassius auratus
goldfish - (species)
Published - Accepted by Curator
Lr21
Pathogen resistance
Coding,
Complex Change
Triticum aestivum
bread wheat - (species)
Domesticated
Linkage Mapping
Huang L; Brooks S; Li W ; et al. (2009)
Evolution of new disease specificity at a simple resistance locus in a crop-weed complex: reconstitu[...]
GP00000551
C5ID17
Physiology
Novel pathogen specificity resulting from chimerism of the parental alleles after intragenic recombination
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species)
Lr21
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
Lr67
Pathogen resistance (rust ; mildew)
Coding,
SNP
Triticum aestivum
bread wheat - (species) D
Domesticated
Linkage Mapping
Moore JW; Herrera-Foessel S; Lan C ; et al. (2015)
A recently evolved hexose transporter variant confers resistance to multiple pathogens in wheat.
GP00001535
A0A0S1LH45
Physiology
Gly144Arg (exon 2) leads to a protein incapable of glucose import; LR67res exerts a dominant-negative effect through heterodimerization with these functional transporters to reduce glucose uptake.; alterations in hexose transport in infected leaves may explain its ability to reduce the growth of multiple biotrophic pathogen species
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species) D
Lr67
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
Lysine histidine transporter 1
Pathogen resistance
Coding,
Insertion
N
Zea mays
(species) D
Domesticated
Linkage Mapping
Zhao Y; Lu X; Liu C ; et al. (2012)
Identification and fine mapping of rhm1 locus for resistance to Southern corn leaf blight in maize.
GP00000555
LHT1
Q9FKS8
Physiology
354bp insertioin resulting in premature stop codon N
Zea mays
(species)
Zea mays
(species) D
Lysine histidine transporter 1
Zea mays
(species)
Published - Accepted by Curator
MATE1/AltSB/SbMATE
Metal tolerance
Cis-regulatory,
Unknown
Sorghum bicolor
sorghum - (species)
Domesticated
Linkage Mapping
Magalhaes JV; Liu J; Guimarães CT ; et al. (2007)
A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sor[...]
GP00000565
Physiology
unknown
Sorghum bicolor
sorghum - (species)
Sorghum bicolor
sorghum - (species)
MATE1/AltSB/SbMATE
Sorghum bicolor
sorghum - (species)
Published - Accepted by Curator
MATE1/ZmMATE1
Metal tolerance
Unknown,
Unknown
Zea mays
(species)
Domesticated
Candidate Gene
Maron LG; Piñeros MA; Guimarães CT ; et al. (2010)
Two functionally distinct members of the MATE (multi-drug and toxic compound extrusion) family of tr[...]
GP00000566
Physiology
unknown
Zea mays
(species)
Zea mays
(species)
MATE1/ZmMATE1
Zea mays
(species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Klungland H; Våge DI; Gomez-Raya L ; et al. (1995)
The role of melanocyte-stimulating hormone (MSH) receptor in bovine coat color determination.
1 Additional References
GP00000571
MC1R
Q01726
Morphology
1 bp deletion at 104: frameshift and premature stop at amino acid 156 N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
MC1R
Bos taurus
cattle - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Klungland H; Våge DI; Gomez-Raya L ; et al. (1995)
The role of melanocyte-stimulating hormone (MSH) receptor in bovine coat color determination.
GP00000572
MC1R
Q01726
Morphology
L99P ; presumably constitutively active - g.14757910T>C c.296T>C p.L99P
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
MC1R
Bos taurus
cattle - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Newton JM; Wilkie AL; He L ; et al. (2000)
Melanocortin 1 receptor variation in the domestic dog.
1 Additional References
GP00000573
MC1R
Q01726
Morphology
R306ter; deletes 12 of 17 a.a. from C-terminus
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
MC1R
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Schmutz SM; Berryere TG; Ellinwood NM ; et al. (2003 Jan-Feb)
MC1R studies in dogs with melanistic mask or brindle patterns.
GP00000574
MC1R
Q01726
Morphology
M264V
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
MC1R
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
Gene Loss,
Complex Change
N
Cavia porcellus
domestic guinea pig - (species) D
Domesticated
Candidate Gene
Cone RD; Lu D; Koppula S ; et al. (1996)
The melanocortin receptors: agonists, antagonists, and the hormonal control of pigmentation.
GP00000575
MC1R
Q01726
Morphology
Deletion of part or all of gene N
Cavia porcellus
domestic guinea pig - (species)
Cavia porcellus
domestic guinea pig - (species) D
MC1R
Cavia porcellus
domestic guinea pig - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
N
Mus musculus
house mouse - (species) D
Domesticated
Candidate Gene
Robbins LS; Nadeau JH; Johnson KR ; et al. (1993)
Pigmentation phenotypes of variant extension locus alleles result from point mutations that alter MS[...]
GP00000582
MC1R
Q01726
Morphology
1bp deletion at 183; frameshift & premature stop N
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species) D
MC1R
Mus musculus
house mouse - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Mus musculus
house mouse - (species)
Domesticated
Candidate Gene
Robbins LS; Nadeau JH; Johnson KR ; et al. (1993)
Pigmentation phenotypes of variant extension locus alleles result from point mutations that alter MS[...]
GP00000584
MC1R
Q01726
Morphology
E92K
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species)
MC1R
Mus musculus
house mouse - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Mus musculus
house mouse - (species)
Domesticated
Candidate Gene
Robbins LS; Nadeau JH; Johnson KR ; et al. (1993)
Pigmentation phenotypes of variant extension locus alleles result from point mutations that alter MS[...]
GP00000585
MC1R
Q01726
Morphology
L98P
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species)
MC1R
Mus musculus
house mouse - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
Deletion
Numida meleagris
helmeted guineafowl - (species) D
Domesticated
Candidate Gene
Vidal O; Araguas RM; Fernández E ; et al. (2010)
Melanism in guinea fowl (Numida meleagris) is associated with a deletion of Phenylalanine-256 in the[...]
GP00000587
MC1R
Q01726
Morphology
Phe256del
Numida meleagris
helmeted guineafowl - (species)
Numida meleagris
helmeted guineafowl - (species) D
MC1R
Numida meleagris
helmeted guineafowl - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Fontanesi L; Tazzoli M; Beretti F ; et al. (2006)
Mutations in the melanocortin 1 receptor (MC1R) gene are associated with coat colours in the domesti[...]
GP00000588
MC1R
Q01726
Morphology
6bp in-frame del of 94-95
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
MC1R
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Fontanesi L; Tazzoli M; Beretti F ; et al. (2006)
Mutations in the melanocortin 1 receptor (MC1R) gene are associated with coat colours in the domesti[...]
GP00000589
MC1R
Q01726
Morphology
30bp in-frame del of 102-111
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
MC1R
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Fontanesi L; Scotti E; Colombo M ; et al. (2010)
A composite six bp in-frame deletion in the melanocortin 1 receptor (MC1R) gene is associated with t[...]
GP00000590
MC1R
Q01726
Morphology
6bp in frame deletion c.[124G>A;125_130del6] + L44T (homozygous state in Japanese, Rhinelander and Dutch tricolour rabbits )
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
MC1R
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Ovis aries
sheep - (species)
Domesticated
Candidate Gene
Våge DI; Klungland H; Lu D ; et al. (1999)
Molecular and pharmacological characterization of dominant black coat color in sheep.
1 Additional References
GP00000591
MC1R
Q01726
Morphology
D121N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species)
MC1R
Ovis aries
sheep - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Ovis aries
sheep - (species)
Domesticated
Candidate Gene
Våge DI; Klungland H; Lu D ; et al. (1999)
Molecular and pharmacological characterization of dominant black coat color in sheep.
1 Additional References
GP00000592
MC1R
Q01726
Morphology
M73K
Ovis aries
sheep - (species)
Ovis aries
sheep - (species)
MC1R
Ovis aries
sheep - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Vulpes vulpes
red fox - (species)
Domesticated
Candidate Gene
Våge DI; Lu D; Klungland H ; et al. (1997)
A non-epistatic interaction of agouti and extension in the fox, Vulpes vulpes.
1 Additional References
GP00000598
MC1R
Q01726
Morphology
C125R; constitutively active receptor
Vulpes vulpes
red fox - (species)
Vulpes vulpes
red fox - (species)
MC1R
Vulpes vulpes
red fox - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Columba livia
rock pigeon - (species)
Domesticated
Candidate Gene
Guernsey MW; Ritscher L; Miller MA ; et al. (2013)
A Val85Met mutation in melanocortin-1 receptor is associated with reductions in eumelanic pigmentati[...]
GP00000601
MC1R
Q01726
Morphology
Val85Met (G253A)
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species)
MC1R
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Coturnix japonica
Japanese quail - (species)
Domesticated
Linkage Mapping
Nadeau NJ; Minvielle F; Mundy NI (2006)
Association of a Glu92Lys substitution in MC1R with extended brown in Japanese quail (Coturnix japon[...]
GP00000602
MC1R
Q01726
Morphology
E92K
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species)
MC1R
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers; eyes)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Linkage Mapping
Takeuchi S; Suzuki H; Yabuuchi M ; et al. (1996)
A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the ch[...]
2 Additional References
GP00000605
MC1R
Q01726
Morphology
E92K; constitutive activation
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
MC1R
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Candidate Gene
Takeuchi S; Suzuki H; Yabuuchi M ; et al. (1996)
A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the ch[...]
GP00000606
MC1R
Q01726
Morphology
C33W
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
MC1R
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Candidate Gene
Takeuchi S; Suzuki H; Yabuuchi M ; et al. (1996)
A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the ch[...]
GP00000607
MC1R
Q01726
Morphology
D37G
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
MC1R
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Candidate Gene
Takeuchi S; Suzuki H; Yabuuchi M ; et al. (1996)
A possible involvement of melanocortin 1-receptor in regulating feather color pigmentation in the ch[...]
GP00000608
MC1R
Q01726
Morphology
L244P
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
MC1R
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Candidate Gene
Kerje S; Lind J; Schütz K ; et al. (2003)
Melanocortin 1-receptor (MC1R) mutations are associated with plumage colour in chicken.
1 Additional References
GP00000609
MC1R
Q01726
Morphology
H215P
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
MC1R
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MC1R
Coloration (skin)
Coding,
Insertion
N
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Linkage Mapping
Kijas JM; Moller M; Plastow G ; et al. (2001)
A frameshift mutation in MC1R and a high frequency of somatic reversions cause black spotting in pig[...]
1 Additional References
GP00000631
MC1R
Q01726
Morphology
2bp insertion at 23 generates early stop @ 56 & D"121"N ? N
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (skin)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Candidate Gene
Kijas JM; Wales R; Törnsten A ; et al. (1998)
Melanocortin receptor 1 (MC1R) mutations and coat color in pigs.
1 Additional References
GP00000632
MC1R
Q01726
Morphology
V"92"M actually at 95
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (skin)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Candidate Gene
Kijas JM; Wales R; Törnsten A ; et al. (1998)
Melanocortin receptor 1 (MC1R) mutations and coat color in pigs.
1 Additional References
GP00000633
MC1R
Q01726
Morphology
D"121"N Actually 124
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (skin)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Candidate Gene
Kijas JM; Wales R; Törnsten A ; et al. (1998)
Melanocortin receptor 1 (MC1R) mutations and coat color in pigs.
1 Additional References
GP00000634
MC1R
Q01726
Morphology
A"161"V actually 164
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (skin)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Candidate Gene
Kijas JM; Wales R; Törnsten A ; et al. (1998)
Melanocortin receptor 1 (MC1R) mutations and coat color in pigs.
1 Additional References
GP00000635
MC1R
Q01726
Morphology
L"99" P Actually 102
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (skin)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Candidate Gene
Kijas JM; Wales R; Törnsten A ; et al. (1998)
Melanocortin receptor 1 (MC1R) mutations and coat color in pigs.
1 Additional References
GP00000636
MC1R
Q01726
Morphology
A"240"T actually 243
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Gustafson NA; Gandolfi B; Lyons LA (2017)
Not another type of potato: MC1R and the russet coloration of Burmese cats.
GP00001330
MC1R
Q01726
Morphology
3bp deletion at c.439-441del (p.Phe146del)
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
MC1R
Felis catus
domestic cat - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Candidate Gene
Rubin CJ; Megens HJ; Martinez Barrio A ; et al. (2012)
Strong signatures of selection in the domestic pig genome.
1 Additional References
GP00001337
MC1R
Q01726
Morphology
c.G>A p.Asp124Asn
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
MC1R
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
2 Mutations:
Coding
SNP
Rangifer tarandus
reindeer - (species) D
Domesticated
Candidate Gene
Våge DI; Nieminen M; Anderson DG ; et al. (2014)
Two missense mutations in melanocortin 1 receptor (MC1R) are strongly associated with dark ventral c[...]
GP00001350
Mc1r
Q01727
Morphology
2 mutations
Rangifer tarandus
reindeer - (species)
Rangifer tarandus
reindeer - (species) D
MC1R
Rangifer tarandus
reindeer - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Equus asinus
ass - (species) D
Domesticated
Candidate Gene
Abitbol M; Legrand R; Tiret L (2014)
A missense mutation in melanocortin 1 receptor is associated with the red coat colour in donkeys.
GP00001351
Mc1r
Q01727
Morphology
c.629T>C p.Met210Thr
Equus asinus
ass - (species)
Equus asinus
ass - (species) D
MC1R
Equus asinus
ass - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Anas platyrhynchos
mallard - (species) D
Domesticated
Candidate Gene
Yu W; Wang C; Xin Q ; et al. (2013)
Non-synonymous SNPs in MC1R gene are associated with the extended black variant in domestic ducks (A[...]
GP00001352
Mc1r
Q01727
Morphology
c.52G>A p.Glu18Lys
Anas platyrhynchos
mallard - (species)
Anas platyrhynchos
mallard - (species) D
MC1R
Anas platyrhynchos
mallard - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
Capra hircus
goat - (species) D
Domesticated
Candidate Gene
Fontanesi L; Beretti F; Riggio V ; et al. (2009)
Missense and nonsense mutations in melanocortin 1 receptor (MC1R) gene of different goat breeds: ass[...]
GP00001353
Mc1r
Q01727
Morphology
c.801C>G p.Cys267Trp
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
MC1R
Capra hircus
goat - (species)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
N
Bos grunniens
domestic yak - (species) D
Domesticated
Candidate Gene
Zhang MQ; Xu X; Luo SJ (2014)
The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens).
GP00001354
Mc1r
Q01727
Morphology
p.Gln34* and p.Met73Leu and p.Arg142Pro - p.Met73Leu and p.Arg142Pro were only found in heterozygous and their association with phenotype is supposed but not sure N
Bos grunniens
domestic yak - (species)
Bos grunniens
domestic yak - (species) D
MC1R
Bos grunniens
domestic yak - (species)
Published - Accepted by Curator
MC1R
Coloration (feathers)
Coding,
SNP
Meleagris gallopavo mexicana
(subspecies) D
Domesticated
Candidate Gene
Vidal O; Viñas J; Pla C (2010)
Variability of the melanocortin 1 receptor (MC1R) gene explains the segregation of the bronze locus [...]
GP00002299
MC1R
Q01726
Morphology
c.364A>T p.I122F
Meleagris gallopavo mexicana
(subspecies)
Meleagris gallopavo mexicana
(subspecies) D
MC1R
Meleagris gallopavo mexicana
(subspecies)
Published - Accepted by Curator
MC1R
Coloration (feathers)
2 Mutations:
Coding
SNP
Meleagris gallopavo mexicana
(subspecies) D
Domesticated
Candidate Gene
Vidal O; Viñas J; Pla C (2010)
Variability of the melanocortin 1 receptor (MC1R) gene explains the segregation of the bronze locus [...]
GP00002300
MC1R
Q01726
Morphology
2 mutations
Meleagris gallopavo mexicana
(subspecies)
Meleagris gallopavo mexicana
(subspecies) D
MC1R
Meleagris gallopavo mexicana
(subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
Deletion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dürig N; Letko A; Lepori V ; et al. (2018)
Two MC1R loss-of-function alleles in cream-coloured Australian Cattle Dogs and white Huskies.
GP00002301
MC1R
Q01726
Morphology
2-bp deletion in the coding sequence c.816_817delCT N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
MC1R
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
Cis-regulatory,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Dürig N; Letko A; Lepori V ; et al. (2018)
Two MC1R loss-of-function alleles in cream-coloured Australian Cattle Dogs and white Huskies.
GP00002302
MC1R
Q01726
Morphology
single nucleotide variant within the MITF binding site of the canine MC1R promoter
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
MC1R
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (coat)
Coding,
SNP
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Dreger DL; Schmutz SM (2010 Sep-Oct)
A new mutation in MC1R explains a coat color phenotype in 2 "old" breeds: Saluki and Afghan hound.
GP00002303
MC1R
Q01726
Morphology
c.233G>T p.G78V N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
MC1R
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
MC1R
Coloration (feathers; eyes)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Candidate Gene
Dávila SG; Gil MG; Resino-Talaván P ; et al. (2014)
Association between polymorphism in the melanocortin 1 receptor gene and E locus plumage color pheno[...]
GP00002390
MC1R
Q01726
Morphology
the Arg213Cys mutation may be the cause of the loss or the decrease of function of the receptor to produce eumelanin
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
MC1R
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MdMYB10
Coloration (fruit flesh; foliage)
Cis-regulatory,
Unknown
Malus domestica
apple - (species)
Domesticated
Linkage Mapping
Chagné D; Carlisle CM; Blond C ; et al. (2007)
Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple.
1 Additional References
GP00000639
MYB1
A0SQ35
Morphology
unknown
Malus domestica
apple - (species)
Malus domestica
apple - (species)
MdMYB10
Malus domestica
apple - (species)
Published - Accepted by Curator
MdMYB110a
Coloration (fruit flesh)
Cis-regulatory,
Unknown
Malus domestica
apple - (species)
Domesticated
Linkage Mapping
Chagné D; Lin-Wang K; Espley RV ; et al. (2013)
An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh p[...]
GP00000640
K4FA06
Morphology
unknown
Malus domestica
apple - (species)
Malus domestica
apple - (species)
MdMYB110a
Malus domestica
apple - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Li W; Sartelet A; Tamma N ; et al. (2016)
Reverse genetic screen for loss-of-function mutations uncovers a frameshifting deletion in the melan[...]
GP00000642
Mlph
Q91V27
Morphology
10bp deletion in exon1 ; c.87_96del p.Glu32Aspfs*1 N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Melanophilin (MLPH)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Bauer A; Kehl A; Jagannathan V ; et al. (2018)
A novel MLPH variant in dogs with coat colour dilution.
GP00000643
Mlph
Q91V27
Morphology
c.705G>C p.Gln235His
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Melanophilin (MLPH)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Linkage Mapping
Ishida Y; David VA; Eizirik E ; et al. (2006)
A homozygous single-base deletion in MLPH causes the dilute coat color phenotype in the domestic cat[...]
GP00000644
Mlph
Q91V27
Morphology
1bp deletion resulting in frameshift c.83delT N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
Melanophilin (MLPH)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
SNP
Gallus gallus
chicken - (species) D
Domesticated
Candidate Gene
Vaez M; Follett SA; Bed'hom B ; et al. (2008)
A single point-mutation within the melanophilin gene causes the lavender plumage colour dilution phe[...]
GP00000645
Mlph
Q91V27
Morphology
c.103C>T p.R35W
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Melanophilin (MLPH)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
Deletion
N
Neovison vison
American mink - (species) D
Domesticated
Candidate Gene
Cirera S; Markakis MN; Christensen K ; et al. (2013)
New insights into the melanophilin (MLPH) gene controlling coat color phenotypes in American mink.
GP00000646
Mlph
Q91V27
Morphology
deletion including intron 7 and exon 8 N
Neovison vison
American mink - (species)
Neovison vison
American mink - (species) D
Melanophilin (MLPH)
Neovison vison
American mink - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
SNP
Neovison vison
American mink - (species) D
Domesticated
Candidate Gene
Cirera S; Markakis MN; Christensen K ; et al. (2013)
New insights into the melanophilin (MLPH) gene controlling coat color phenotypes in American mink.
1 Additional References
GP00000647
Mlph
Q91V27
Morphology
Splice donor site variation in exon 8 resulting in a premature stop codon c.901+1G>A
Neovison vison
American mink - (species)
Neovison vison
American mink - (species) D
Melanophilin (MLPH)
Neovison vison
American mink - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
Deletion
N
Oryctolagus
(genus) D
Domesticated
Candidate Gene
Fontanesi L; Scotti E; Allain D ; et al. (2014)
A frameshift mutation in the melanophilin gene causes the dilute coat colour in rabbit (Oryctolagus [...]
GP00000648
Mlph
Q91V27
Morphology
1bp deletion resulting in frameshift N
Oryctolagus
(genus)
Oryctolagus
(genus) D
Melanophilin (MLPH)
Oryctolagus
(genus)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
SNP
Oryctolagus
(genus) D
Domesticated
Candidate Gene
Lehner S; Gähle M; Dierks C ; et al. (2013)
Two-exon skipping within MLPH is associated with coat color dilution in rabbits.
GP00000649
Mlph
Q91V27
Morphology
c.111-5C>A (exon skipping resulting in frameshift and truncated protein)
Oryctolagus
(genus)
Oryctolagus
(genus) D
Melanophilin (MLPH)
Oryctolagus
(genus)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (feathers)
Unknown,
Complex Change
Coturnix japonica
Japanese quail - (species)
Domesticated
Linkage Mapping
Minvielle F; Cecchi T; Passamonti P ; et al. (2009)
Plumage colour mutations and melanins in the feathers of the Japanese quail: a first comparison.
1 Additional References
GP00000650
Mlph
Q91V27
Morphology
Large deletions and rearrangement with pseudogenization of MLPH and loss of two other genes
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species)
Melanophilin (MLPH)
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Linkage Mapping
Drögemüller C; Philipp U; Haase B ; et al. (2007)
A noncoding melanophilin gene (MLPH) SNP at the splice donor of exon 1 represents a candidate causal[...]
GP00002330
Mlph
Q91V27
Morphology
GA substitution at splice donor site causing Splicing defect
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Melanophilin (MLPH)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
Insertion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Van Buren SL; Minor KM; Grahn RA ; et al. (2020)
A Third MLPH Variant Causing Coat Color Dilution in Dogs.
GP00002331
Mlph
Q91V27
Morphology
c.667_668insC p.(His223Profs*41) N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Melanophilin (MLPH)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Melanophilin (MLPH)
Coloration (coat)
Coding,
Deletion
N
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Lehner S; Gähle M; Dierks C ; et al. (2013)
Two-exon skipping within MLPH is associated with coat color dilution in rabbits.
GP00002332
Mlph
Q91V27
Morphology
c.585delG p.L195LfsX123* N
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
Melanophilin (MLPH)
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
MFSD12
Coloration (coat)
Coding,
Insertion
N
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Tanaka J; Leeb T; Rushton J ; et al. (2019)
Frameshift Variant in MFSD12 Explains the Mushroom Coat Color Dilution in Shetland Ponies.
GP00002243
MFSD12
Q6NUT3
Morphology
p.(Asp201fs) due to c.600Cins N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
MFSD12
Equus caballus
horse - (species)
Published - Accepted by Curator
MFSD12
Coloration (coat)
Coding,
SNP
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Hédan B; Cadieu E; Botherel N ; et al. (2019)
Identification of a Missense Variant in MFSD12 Involved in Dilution of Phaeomelanin Leading to White[...]
GP00002244
MFSD12
Q6NUT3
Morphology
c.151C>T p.Arg51Cys N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
MFSD12
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
MGAM
Starch processing
Cis-regulatory,
Unknown
Canis lupus familiaris
dog - (subspecies)
Domesticated
Association Mapping
Axelsson E; Ratnakumar A; Arendt ML ; et al. (2013)
The genomic signature of dog domestication reveals adaptation to a starch-rich diet.
GP00000654
MGAM
O43451
Physiology
unknown
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies)
MGAM
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Unknown,
Unknown
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Fontanesi L; Scotti E; Russo V (2012)
Haplotype variability in the bovine MITF gene and association with piebaldism in Holstein and Simmen[...]
2 Additional References
GP00000656
Mitf
Q08874
Morphology
unknown but association with intronic variant
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Microphtalmia-associated transcription factor
Bos taurus
cattle - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Cis-regulatory,
Deletion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Karlsson EK; Baranowska I; Wade CM ; et al. (2007)
Efficient mapping of mendelian traits in dogs through genome-wide association.
1 Additional References
GP00000657
Mitf
Q08874
Morphology
g.21836232_21836427ins>del - this SINE-insertion variant is the first of three possible regulatory variants described by Karlsson et al. (2007). Its genomic location and description were kindly provided by Professor Claire Wade in August 2018. OMIA 000214-9615
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Microphtalmia-associated transcription factor
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Cis-regulatory,
Insertion
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Haase B; Blatter M ; et al. (2012)
Mutations in MITF and PAX3 cause "splashed white" and other white spotting phenotypes in horses.
GP00000658
Mitf
Q08874
Morphology
11bp insertion in melanocyte-specific promoter; disrupting PAX3 binding site
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Microphtalmia-associated transcription factor
Equus caballus
horse - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Haase B; Blatter M ; et al. (2012)
Mutations in MITF and PAX3 cause "splashed white" and other white spotting phenotypes in horses.
GP00000659
Mitf
Q08874
Morphology
c.629A>G N310S yielding defective DNA-binding
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Microphtalmia-associated transcription factor
Equus caballus
horse - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (feathers)
Coding,
Deletion
N
Coturnix japonica
Japanese quail - (species) D
Domesticated
Candidate Gene
Minvielle F; Bed'hom B; Coville JL ; et al. (2010)
The "silver" Japanese quail and the MITF gene: causal mutation, associated traits and homology with [...]
1 Additional References
GP00000660
Mitf
Q08874
Morphology
2bp deletion N
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species) D
Microphtalmia-associated transcription factor
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (feathers)
Cis-regulatory,
Insertion
Anas platyrhynchos
mallard - (species) D
Domesticated
Linkage Mapping
Zhou Z; Li M; Cheng H ; et al. (2018)
An intercross population study reveals genes associated with body size and plumage color in ducks.
GP00002127
Mitf
Q08874
Morphology
6.6kb insertion between exon 1M and exon 2, leads to lower expression of isoform MITF M in pekin white ducks
Anas platyrhynchos
mallard - (species)
Anas platyrhynchos
mallard - (species) D
Microphtalmia-associated transcription factor
Anas platyrhynchos
mallard - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Haase B; Blatter M ; et al. (2012)
Mutations in MITF and PAX3 cause "splashed white" and other white spotting phenotypes in horses.
GP00002322
Mitf
Q08874
Morphology
c.519_523delGTGTC p.C174Sfs*20 N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Microphtalmia-associated transcription factor
Equus caballus
horse - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Dürig N; Jude R; Jagannathan V ; et al. (2017)
A novel MITF variant in a white American Standardbred foal.
GP00002323
Mitf
Q08874
Morphology
c.731G>A p.G244E
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Microphtalmia-associated transcription factor
Equus caballus
horse - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Henkel J; Lafayette C; Brooks SA ; et al. (2019)
Whole-genome sequencing reveals a large deletion in the MITF gene in horses with white spotted coat [...]
GP00002324
Mitf
Q08874
Morphology
~63-kb deletion spanning exons 6-9 N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Microphtalmia-associated transcription factor
Equus caballus
horse - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Magdesian KG; Tanaka J; Bellone RR (2020)
A De Novo MITF Deletion Explains a Novel Splashed White Phenotype in an American Paint Horse.
GP00002325
Mitf
Q08874
Morphology
8.7 kb deletion N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Microphtalmia-associated transcription factor
Equus caballus
horse - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Unknown,
Unknown
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Hofstetter S; Seefried F; Häfliger IM ; et al. (2019)
A non-coding regulatory variant in the 5'-region of the MITF gene is associated with white-spotted c[...]
GP00002326
Mitf
Q08874
Morphology
unknown based SNP association
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Microphtalmia-associated transcription factor
Bos taurus
cattle - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
SNP
N
Bubalus bubalis
water buffalo - (species) D
Domesticated
Candidate Gene
Yusnizar Y; Wilbe M; Herlino AO ; et al. (2015)
Microphthalmia-associated transcription factor mutations are associated with white-spotted coat colo[...]
GP00002327
Mitf
Q08874
Morphology
c.328C>T p.R110* N
Bubalus bubalis
water buffalo - (species)
Bubalus bubalis
water buffalo - (species) D
Microphtalmia-associated transcription factor
Bubalus bubalis
water buffalo - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor
Coloration (coat)
Coding,
SNP
N
Bubalus bubalis
water buffalo - (species) D
Domesticated
Candidate Gene
Yusnizar Y; Wilbe M; Herlino AO ; et al. (2015)
Microphthalmia-associated transcription factor mutations are associated with white-spotted coat colo[...]
GP00002328
Mitf
Q08874
Morphology
donor splice-site mutation leads to aberrant splicing of exon 8 that encodes part of a highly conserved region of MITF N
Bubalus bubalis
water buffalo - (species)
Bubalus bubalis
water buffalo - (species) D
Microphtalmia-associated transcription factor
Bubalus bubalis
water buffalo - (species)
Published - Accepted by Curator
Microphtalmia-associated transcription factor a (MITFA)
Coloration (amelanism)
Cis-regulatory,
Deletion
Betta splendens
Siamese fighting fish - (species) D
Domesticated
Linkage Mapping
Wang L; Sun F; Wan ZY ; et al. (2021)
Genomic Basis of Striking Fin Shapes and Colors in the Fighting Fish.
GP00002379
Q6P0E9NULL
Morphology
"Comparison between homozygous albino and wild-type pigmented fish revealed a cluster of indels and SNPs about 25 kb upstream of mitfa, including a 366-bp deletion in the albino mutant. Genotyping this deletion in ∼1,000 fish revealed that this deletion was strictly correlated with the albino phenotype (supplementary fig. S14 and table S9, Supplementary Material online). These data suggest that the 366-bp deletion is a distant cis-regulatory element and could underlie the albino phenotype."
Betta splendens
Siamese fighting fish - (species)
Betta splendens
Siamese fighting fish - (species) D
Microphtalmia-associated transcription factor a (MITFA)
Betta splendens
Siamese fighting fish - (species)
Published - Accepted by Curator
miR-15a-16
Body size (weight)
Cis-regulatory,
Insertion
N
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Jia X; Lin H; Nie Q ; et al. (2016)
A short insertion mutation disrupts genesis of miR-16 and causes increased body weight in domesticat[...]
GP00002247
Morphology
54-bp insertion introducing splicing site that affect the mature transcript N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
miR-15a-16
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MKT1
Temperature tolerance
Virulence
Sporulation efficiency
Sporulation efficiency
Xenobiotic resistance (alcohol; ethanol)
Xenobiotic resistance (genotoxic DNA-damage agent)
Coding,
SNP
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Steinmetz LM; Sinha H; Richards DR ; et al. (2002)
Dissecting the architecture of a quantitative trait locus in yeast.
5 Additional References
GP00000666
MKT1
P40850
Physiology
Physiology
Physiology
Physiology
Physiology
Physiology
G30D (functionally verified); or haplotype including G30D (functionally verified)
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
MKT1
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
Mla (=Sr33/AetRGA1e)
Pathogen resistance
Coding,
Unknown
Aegilops tauschii
(species)
Domesticated
Linkage Mapping
Periyannan S; Moore J; Ayliffe M ; et al. (2013)
The gene Sr33, an ortholog of barley Mla genes, encodes resistance to wheat stem rust race Ug99.
GP00000667
Mla1
Q7EXP5
Physiology
Unknown
Triticum aestivum
bread wheat - (species)
Aegilops tauschii
(species)
Mla (=Sr33/AetRGA1e)
Aegilops tauschii
(species)
Published - Accepted by Curator
Mla1
Pathogen resistance
Coding,
SNP
Hordeum vulgare
(species)
Domesticated
Linkage Mapping
Mahadevappa M; Descenzo RA; Wise RP (1994)
Recombination of alleles conferring specific resistance to powdery mildew at the Mla locus in barley[...]
3 Additional References
GP00000668
Mla1
Q7EXP5
Physiology
Coding variation in the LRR domain - exact amino acid change unknown
Hordeum vulgare
(species)
Hordeum vulgare
(species)
Mla1
Hordeum vulgare
(species)
Published - Accepted by Curator
Mla1
Pathogen resistance
Coding,
Unknown
Triticum monococcum
(species)
Domesticated
Candidate Gene
Halterman D; Zhou F; Wei F ; et al. (2001)
The MLA6 coiled-coil, NBS-LRR protein confers AvrMla6-dependent resistance specificity to Blumeria g[...]
1 Additional References
GP00000669
Mla1
Q7EXP5
Physiology
Coding variation in the LRR domain
Triticum monococcum
(species)
Triticum monococcum
(species)
Mla1
Triticum monococcum
(species)
Published - Accepted by Curator
Mla13
Pathogen resistance
Coding,
SNP
Hordeum vulgare
(species)
Domesticated
Linkage Mapping
Mahadevappa M; Descenzo RA; Wise RP (1994)
Recombination of alleles conferring specific resistance to powdery mildew at the Mla locus in barley[...]
2 Additional References
GP00000670
Mla1
Q7EXP5
Physiology
Coding variation in the LRR domain - exact amino acid change unknown
Hordeum vulgare
(species)
Hordeum vulgare
(species)
Mla13
Hordeum vulgare
(species)
Published - Accepted by Curator
Mla6
Pathogen resistance
Coding,
SNP
Hordeum vulgare
(species)
Domesticated
Linkage Mapping
Mahadevappa M; Descenzo RA; Wise RP (1994)
Recombination of alleles conferring specific resistance to powdery mildew at the Mla locus in barley[...]
2 Additional References
GP00000671
Mla1
Q7EXP5
Physiology
Coding variation in the LRR domain - exact amino acid change(s) unknown
Hordeum vulgare
(species)
Hordeum vulgare
(species)
Mla6
Hordeum vulgare
(species)
Published - Accepted by Curator
Mlana
Coloration (feathers ; white-spotting)
Gene Amplification,
Complex Change
Columba livia
rock pigeon - (species) D
Domesticated
Association Mapping
Bruders R; Van Hollebeke H; Osborne EJ ; et al. (2020)
A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Col[...]
GP00002342
MLANA
Q16655
Morphology
CNV with 7 copies of the outer 77-kb segment and 14 copies of the inner 25-kb segment in the genomes of female (ZStW) Almond pigeons
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
Mlana
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
MLO
Pathogen resistance
Gene Amplification,
Insertion
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Piffanelli P; Ramsay L; Waugh R ; et al. (2004)
A barley cultivation-associated polymorphism conveys resistance to powdery mildew.
GP00000672
MLO
P93766
Physiology
Tandem array duplication including promoter and partial CDS; resulting in loss-of-function by transcriptional interference
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
MLO
Hordeum vulgare
(species)
Published - Accepted by Curator
MLO1
Pathogen resistance
Coding,
SNP
N
Pisum sativum
pea - (species)
Domesticated
Linkage Mapping
Pavan S; Schiavulli A; Appiano M ; et al. (2011)
Pea powdery mildew er1 resistance is associated to loss-of-function mutations at a MLO homologous lo[...]
GP00000673
MLO
P93766
Physiology
1bp substitution resulting in premature stop codon N
Pisum sativum
pea - (species)
Pisum sativum
pea - (species)
MLO1
Pisum sativum
pea - (species)
Published - Accepted by Curator
MLO1
Pathogen resistance
Coding,
Deletion
N
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Bai Y; Pavan S; Zheng Z ; et al. (2008)
Naturally occurring broad-spectrum powdery mildew resistance in a Central American tomato accession [...]
GP00000674
MLO
P93766
Physiology
19bp deletion resulting in frameshift N
Solanum lycopersicum
tomato - (species)
Solanum lycopersicum
tomato - (species) D
MLO1
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
MNR2
Bird head comb
Fertility (sperm motility)
Gene Amplification,
Inversion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Imsland F; Feng C; Boije H ; et al. (2012)
The Rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb [...]
GP00000675
MNR2
Q9YHY8
Morphology
Physiology
7.4Mb inversion (and secondary structural re-arrangement in some individuals)
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
MNR2
Gallus gallus
chicken - (species)
Published - Accepted by Curator
MRC2
Muscular mass
Tail shape (crooked ; defect)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Fasquelle C; Sartelet A; Li W ; et al. (2009)
Balancing selection of a frame-shift mutation in the MRC2 gene accounts for the outbreak of the Croo[...]
2 Additional References
GP00002264
MRC2
Q9UBG0
Physiology
Morphology
c.2904-2905delAG p.Gly934X N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
MRC2
Bos taurus
cattle - (species)
Published - Accepted by Curator
MRC2
Muscular mass
Tail shape (crooked ; defect)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Fasquelle C; Sartelet A; Li W ; et al. (2009)
Balancing selection of a frame-shift mutation in the MRC2 gene accounts for the outbreak of the Croo[...]
2 Additional References
GP00002265
MRC2
Q9UBG0
Physiology
Morphology
c.1906T>G p.C636G
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
MRC2
Bos taurus
cattle - (species)
Published - Accepted by Curator
MSH4
Recombination rate (female)
Unknown,
Unknown
Bos taurus
cattle - (species)
Domesticated
Association Mapping
Ma L; O'Connell JR; VanRaden PM ; et al. (2015)
Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.
GP00001665
MSH4
E1BK76
Physiology
On chromosome 3. Associated SNP located in the intron of the gene
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
MSH4
Bos taurus
cattle - (species)
Published - Accepted by Curator
mucilage-modified 2 (mum2)
Mucilage (seeds)
Coding,
Deletion
N
Arabidopsis thaliana
thale cress - (species) D
Domesticated
Linkage Mapping
Macquet A; Ralet MC; Loudet O ; et al. (2007)
A naturally occurring mutation in an Arabidopsis accession affects a beta-D-galactosidase that incre[...]
GP00000681
BGAL6
Q9FFN4
Physiology
44bp deletion in exon 15; from Leu-662 onwards. This deletion causes a frame-shift mutation changing the next 23 amino acids followed by the introduction of a stop codon. N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
mucilage-modified 2 (mum2)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
MuPKS
Coloration (psittacofulvin; feathers)
Coding,
SNP
Melopsittacus undulatus
budgerigar - (species) D
Domesticated
Association Mapping
Cooke TF; Fischer CR; Wu P ; et al. (2017)
Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars.
GP00002121
PKS15
A0A218V6J0
Morphology
Melopsittacus undulatus
budgerigar - (species)
Melopsittacus undulatus
budgerigar - (species) D
MuPKS
Melopsittacus undulatus
budgerigar - (species)
Published - Accepted by Curator
Muscle-specific adenosine monophosphate-activated protein kinase (PRKAG3)
Glycogen content (muscles)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Linkage Mapping
Milan D; Jeon JT; Looft C ; et al. (2000)
A mutation in PRKAG3 associated with excess glycogen content in pig skeletal muscle.
GP00000682
Prkag3
Q8BGM7
Physiology
R200Q in CBS1; which is the most conserved region among AMPK g chain isoforms; and R200 is conserved in mammalian and Drosophila AMPK g isoforms
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
Muscle-specific adenosine monophosphate-activated protein kinase (PRKAG3)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Muscle-specific adenosine monophosphate-activated protein kinase (PRKAG3)
Glycogen content (muscles)
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Candidate Gene
Ciobanu D; Bastiaansen J; Malek M ; et al. (2001)
Evidence for new alleles in the protein kinase adenosine monophosphate-activated gamma(3)-subunit ge[...]
GP00002333
Prkag3
Q8BGM7
Physiology
p.(I249V)
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
Muscle-specific adenosine monophosphate-activated protein kinase (PRKAG3)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
MYB1
Coloration (inner flesh)
Cis-regulatory,
Unknown
Beta vulgaris
(species)
Domesticated
Candidate Gene
Hatlestad GJ; Akhavan NA; Sunnadeniya RM ; et al. (2015)
The beet Y locus encodes an anthocyanin MYB-like protein that activates the betalain red pigment pat[...]
GP00001396
MYB1
M1ETA5
Physiology
unknown mutations within 460bp of putative 5 prime UTR
Beta vulgaris
(species)
Beta vulgaris
(species)
MYB1
Beta vulgaris
(species)
Published - Accepted by Curator
MYB1
Coloration (flowers; seeds; stems)
Coding,
Deletion
N
Ipomoea nil
Japanese morning glory - (species) D
Domesticated
Candidate Gene
Morita Y; Saitoh M; Hoshino A ; et al. (2006)
Isolation of cDNAs for R2R3-MYB, bHLH and WDR transcriptional regulators and identification of c and[...]
GP00002089
myb1
Q4QS21
Morphology
frameshift mutation caused by a 2 bp deletion N
Ipomoea nil
Japanese morning glory - (species)
Ipomoea nil
Japanese morning glory - (species) D
MYB1
Ipomoea nil
Japanese morning glory - (species)
Published - Accepted by Curator
MYB1
Coloration (inner flesh)
Cis-regulatory,
Epigenetic Change
Raphanus sativus
radish - (species) D
Domesticated
Candidate Gene
Wang Q; Wang Y; Sun H ; et al. (2020)
Transposon-induced methylation of the RsMYB1 promoter disturbs the anthocyanin accumulation in red-f[...]
GP00002094
MYB1
M1ETA5
Physiology
The taproot white-fleshed mutant is the result of altered DNA methylation in the RsMYB1 promoter. This heritable epigenetic change is due to a hypermethylated CACTA transposon (a 7372-bp TE) which induces the spreading of DNA methylation to the promoter region of RsMYB1. RsMYB1 expression is considerably downregulated and this inhibits anthocyanin biosynthesis in white-fleshed mutants.
Raphanus sativus
radish - (species)
Raphanus sativus
radish - (species) D
MYB1
Raphanus sativus
radish - (species)
Published - Accepted by Curator
Myosin heavy chain 9
Heat tolerance
Racing performance
Cis-regulatory,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Huson HJ; vonHoldt BM; Rimbault M ; et al. (2012)
Breed-specific ancestry studies and genome-wide association analysis highlight an association betwee[...]
GP00000684
MYH9
P35579
Physiology
Physiology
Several candidate SNPs - exact causing mutation(s) unknown
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Myosin heavy chain 9
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Grobet L; Martin LJ; Poncelet D ; et al. (1997)
A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle.
2 Additional References
GP00000685
MSTN
O14793
Morphology
nt821 11bp deletion c.821-831delTGAACACTCCA p.Glu275ArgfsX14 N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
Indel
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Grobet L; Poncelet D; Royo LJ ; et al. (1998)
Molecular definition of an allelic series of mutations disrupting the myostatin function and causing[...]
GP00000686
MSTN
O14793
Morphology
nt419 7bp deletion and 10bp insertion; leading to a premature stop codon at position 140 c.419_425del7, c418_426ins10 N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Grobet L; Poncelet D; Royo LJ ; et al. (1998)
Molecular definition of an allelic series of mutations disrupting the myostatin function and causing[...]
GP00000687
MSTN
O14793
Morphology
c.610C>T p.Q204* N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Grobet L; Poncelet D; Royo LJ ; et al. (1998)
Molecular definition of an allelic series of mutations disrupting the myostatin function and causing[...]
GP00000688
MSTN
O14793
Morphology
E226* caused by G676T N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
McPherron AC; Lee SJ (1997)
Double muscling in cattle due to mutations in the myostatin gene.
2 Additional References
GP00000689
MSTN
O14793
Morphology
C313Y caused by G938A; disrupts disulphide bond
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Marchitelli C; Savarese MC; Crisà A ; et al. (2003)
Double muscling in Marchigiana beef breed is caused by a stop codon in the third exon of myostatin g[...]
GP00000690
MSTN
O14793
Morphology
E291* caused by G>T N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Alexander LJ; Kuehn LA; Smith TP ; et al. (2009)
A Limousin specific myostatin allele affects longissimus muscle area and fatty acid profiles in a Wa[...]
GP00000692
MSTN
O14793
Morphology
c.282C>A p.Phe94Leu
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
Deletion
N
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Boman IA; Klemetsdal G; Blichfeldt T ; et al. (2009)
A frameshift mutation in the coding region of the myostatin gene (MSTN) affects carcass conformation[...]
GP00000693
MSTN
O14793
Morphology
1bp deletion resulting in a premature stop codon at position 320 N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
Myostatin (MSTN = GDF8)
Ovis aries
sheep - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
Insertion
N
Ovis aries
sheep - (species) D
Domesticated
Candidate Gene
Boman IA; Våge DI (2009)
An insertion in the coding region of the myostatin (MSTN) gene affects carcass conformation and fatn[...]
GP00000694
MSTN
O14793
Morphology
1bp insertion resulting in premature stop codon at position 49 N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
Myostatin (MSTN = GDF8)
Ovis aries
sheep - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Cis-regulatory,
SNP
Ovis aries
sheep - (species)
Domesticated
Linkage Mapping
Clop A; Marcq F; Takeda H ; et al. (2006)
A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects musc[...]
GP00000695
MSTN
O14793
Morphology
1bp change; generates binding site for two muscle-expressed miRNAs; causing mRNA degradation and lower levels of circulating myostatin
G to A transition in the 3' UTR that creates a target site for mir1 and mir206 microRNAs
Ovis aries
sheep - (species)
Ovis aries
sheep - (species)
Myostatin (MSTN = GDF8)
Ovis aries
sheep - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Cis-regulatory,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Candidate Gene
Stinckens A; Luyten T; Bijttebier J ; et al. (2008)
Characterization of the complete porcine MSTN gene and expression levels in pig breeds differing in [...]
GP00000696
MSTN
O14793
Morphology
Possible promoter disruption ; changes the G nucleotide at position 8 of the MEF3 binding site into an A nucleotide, thus disrupting the MEF3 binding site
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
Myostatin (MSTN = GDF8)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Racing performance
Coding,
Deletion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Mosher DS; Quignon P; Bustamante CD ; et al. (2007)
A mutation in the myostatin gene increases muscle mass and enhances racing performance in heterozygo[...]
GP00000697
MSTN
O14793
Morphology; Physiology
2bp deletion in the third exon c.939_940delTG p.C313* N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
Myostatin (MSTN = GDF8)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Racing performance
Cis-regulatory,
Insertion
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Binns MM; Boehler DA; Lambert DH (2010)
Identification of the myostatin locus (MSTN) as having a major effect on optimum racing distance in [...]
3 Additional References
GP00000698
MSTN
O14793
Morphology; Physiology
227-bp SINE insertion in promoter
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Myostatin (MSTN = GDF8)
Equus caballus
horse - (species)
Published - Accepted by Curator
Myostatin (MSTN = GDF8)
Muscular mass (double muscling)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Dierks C; Eder J; Glatzer S ; et al. (2015)
A novel myostatin mutation in double-muscled German Gelbvieh.
GP00002248
MSTN
O14793
Morphology
c.191T>C p.L64P
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Myostatin (MSTN = GDF8)
Bos taurus
cattle - (species)
Published - Accepted by Curator
NAM-B1 (=Gpc-B1)
Grain content
Senescence (grain)
Coding,
Insertion
N
Triticum turgidum
(species) D
Domesticated
Linkage Mapping
Uauy C; Distelfeld A; Fahima T ; et al. (2006)
A NAC Gene regulating senescence improves grain protein, zinc, and iron content in wheat.
GP00000717
NAM-B1
A0SPJ4
Physiology
Physiology
1bp insertion resulting in frameshift N
Triticum turgidum
(species)
Triticum turgidum
(species) D
NAM-B1 (=Gpc-B1)
Triticum turgidum
(species)
Published - Accepted by Curator
NCED4
Seed dormancy
Unknown,
Unknown
Lactuca sativa
(species) D
Domesticated
Linkage Mapping
Argyris J; Truco MJ; Ochoa O ; et al. (2011)
A gene encoding an abscisic acid biosynthetic enzyme (LsNCED4) collocates with the high temperature [...]
1 Additional References
GP00000737
CCD4
O49675
Physiology
unknown
Lactuca serriola
(species)
Lactuca sativa
(species) D
NCED4
Lactuca sativa
(species)
Published - Accepted by Curator
ndp (norrin)
Coloration (plumage)
Coding,
SNP
N
Columba livia
rock pigeon - (species) D
Domesticated
Association Mapping
Vickrey AI; Bruders R; Kronenberg Z ; et al. (2018)
Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity i[...]
GP00002250
Ndp
P48744
Morphology
Start-codon change predicted to truncate the amino terminus of the NDP protein by 11 amino acids thereby disrupting the 24-amino acid signal peptide sequence N
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
ndp (norrin)
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
NEK9
Recombination rate
Unknown,
Unknown
Bos taurus
cattle - (species)
Domesticated
Association Mapping
Ma L; O'Connell JR; VanRaden PM ; et al. (2015)
Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.
GP00001663
NEK9
F1MM88
Physiology
On chromosome 10. Associated SNP located 10 kb dowstream
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
NEK9
Bos taurus
cattle - (species)
Published - Accepted by Curator
Nramp aluminum transporter1
Metal tolerance
2 Mutations:
Coding
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Famoso AN; Zhao K; Clark RT ; et al. (2011)
Genetic architecture of aluminum tolerance in rice (Oryza sativa) determined through genome-wide ass[...]
GP00000740
NRAT1
Q6ZG85
Physiology
2 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Nramp aluminum transporter1
Oryza sativa
rice - (species)
Published - Accepted by Curator
NRT1.1B
Nitrogen use (metabolism)
Coding,
SNP
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Hu B; Wang W; Ou S ; et al. (2015)
Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies.
GP00001375
NPF6.3
Q05085
Physiology
c.980C>T p.Met327Thr
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
NRT1.1B
Oryza sativa
rice - (species)
Published - Accepted by Curator
NUDT7
Meat color
Cis-regulatory,
Unknown
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Taniguchi M; Hayashi T; Nii M ; et al. (2010)
Fine mapping of quantitative trait loci for meat color on Sus scrofa chromosome 6: analysis of the s[...]
1 Additional References
GP00000741
Nudt7
Q99P30
Physiology
unknown
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
NUDT7
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
nurf-1
Fertility (reproductive timing; egg laying rate)
Lifespan
Growth rate
Diapause (dauer formation)
Coding,
Deletion
Caenorhabditis elegans
(species) D
Domesticated
Linkage Mapping
Large EE; Xu W; Zhao Y ; et al. (2016)
Selection on a Subunit of the NURF Chromatin Remodeler Modifies Life History Traits in a Domesticate[...]
GP00001318
nurf-1
Q6BER5
Physiology
Physiology
Physiology
Physiology
60bp deletion
Caenorhabditis elegans
(species)
Caenorhabditis elegans
(species) D
nurf-1
Caenorhabditis elegans
(species)
Published - Accepted by Curator
Oca2
Coloration (albinism)
Coding,
Insertion
N
Carassius auratus
goldfish - (species) D
Domesticated
Candidate Gene
Kon T; Omori Y; Fukuta K ; et al. (2020)
The Genetic Basis of Morphological Diversity in Domesticated Goldfish.
GP00002351
Oca2
Q62052
Morphology
1-bp insert creating a frameshift and a truncated protein (470 amino acids instead of 805). In oca2L ohnolog on chromosome LG6. N
Carassius auratus
goldfish - (species)
Carassius auratus
goldfish - (species) D
Oca2
Carassius auratus
goldfish - (species)
Published - Accepted by Curator
Oca2
Coloration (albinism)
Coding,
Deletion
N
Carassius auratus
goldfish - (species) D
Domesticated
Candidate Gene
Kon T; Omori Y; Fukuta K ; et al. (2020)
The Genetic Basis of Morphological Diversity in Domesticated Goldfish.
GP00002352
Oca2
Q62052
Morphology
1-bp deletion creating a frameshift and a truncated protein (519 amino acids instead of 805). In oca2S ohnolog on chromosome LG31. N
Carassius auratus
goldfish - (species)
Carassius auratus
goldfish - (species) D
Oca2
Carassius auratus
goldfish - (species)
Published - Accepted by Curator
ODORANT1 [pseudo-replication between 2 ODO1 entries due to possible homology between alleles]
Fragrance
Cis-regulatory,
SNP
Petunia x hybrida
(species)
Domesticated
Linkage Mapping
Van Moerkercke A; Haring MA; Schuurink RC (2011)
The transcription factor EMISSION OF BENZENOIDS II activates the MYB ODORANT1 promoter at a MYB bind[...]
GP00000751
ODO1
Q50EX6
Physiology
C/T substitution in enhancer region MYB-TF binding site
Petunia x hybrida
(species)
Petunia x hybrida
(species)
ODORANT1 [pseudo-replication between 2 ODO1 entries due to possible homology between alleles]
Petunia x hybrida
(species)
Published - Accepted by Curator
opaque2 (O2)
Lysine content (endosperm)
Coding,
Deletion
N
Zea mays
(species) D
Domesticated
Linkage Mapping
Schmidt RJ; Burr FA; Burr B (1987)
Transposon tagging and molecular analysis of the maize regulatory locus opaque-2.
1 Additional References
GP00000753
O2
P12959
Physiology
1bp deletion predicted to cause premature termination of translation N
Zea mays
(species)
Zea mays
(species) D
opaque2 (O2)
Zea mays
(species)
Published - Accepted by Curator
opaque2 (O2)
Lysine content (endosperm)
Cis-regulatory,
Insertion
Zea mays
(species) D
Domesticated
Linkage Mapping
Schmidt RJ; Burr FA; Burr B (1987)
Transposon tagging and molecular analysis of the maize regulatory locus opaque-2.
GP00000754
O2
P12959
Physiology
insertion of a non-autonomous rbg transposable element in the untranslated leader sequence of the O2 gene
Zea mays
(species)
Zea mays
(species) D
opaque2 (O2)
Zea mays
(species)
Published - Accepted by Curator
Os07g0603400
Grain size
Grain quality
2 Mutations:
Coding
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Wang Y; Xiong G; Hu J ; et al. (2015)
Copy number variation at the GL7 locus contributes to grain size diversity in rice.
GP00001542
Os07g0603400
A3BLY4
Morphology
Physiology
2 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Os07g0603400
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsC1
Coloration (loss of apiculus color)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Saitoh K; Onishi K; Mikami I ; et al. (2004)
Allelic diversification at the C (OsC1) locus of wild and cultivated rice: nucleotide changes associ[...]
2 Additional References
GP00000805
C
Q76B79
Morphology
10bp deletion N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
OsC1
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsC1
Coloration (loss of apiculus color)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Saitoh K; Onishi K; Mikami I ; et al. (2004)
Allelic diversification at the C (OsC1) locus of wild and cultivated rice: nucleotide changes associ[...]
2 Additional References
GP00000806
C
Q76B79
Morphology
2bp deletion N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
OsC1
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsCKX2=Gn1a
Grain yield
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Ashikari M; Sakakibara H; Lin S ; et al. (2005)
Cytokinin oxidase regulates rice grain production.
GP00000807
CKX2
Q4ADV8
Morphology
11bp deletion causing premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
OsCKX2=Gn1a
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsCKX2=Gn1a
Grain yield
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Ashikari M; Sakakibara H; Lin S ; et al. (2005)
Cytokinin oxidase regulates rice grain production.
GP00000808
CKX2
Q4ADV8
Morphology
Not identified
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsCKX2=Gn1a
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsCKX2=Gn1a
Grain yield
Cis-regulatory,
Unknown
Triticum aestivum
bread wheat - (species)
Domesticated
Linkage Mapping
Zhang L; Zhao YL; Gao LF ; et al. (2012)
TaCKX6-D1, the ortholog of rice OsCKX2, is associated with grain weight in hexaploid wheat.
GP00000809
CKX2
Q4ADV8
Morphology
unknown
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species)
OsCKX2=Gn1a
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
OsGA20ox1
Seedling vigor
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Abe A; Takagi H; Fujibe T ; et al. (2012)
OsGA20ox1, a candidate gene for a major QTL controlling seedling vigor in rice.
GP00000810
GA20OX1
P93771
Physiology
unknown ; no coding variation
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsGA20ox1
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsLG1
Seed shattering (panicle shape)
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Ishii T; Numaguchi K; Miura K ; et al. (2013)
OsLG1 regulates a closed panicle trait in domesticated rice.
GP00000811
SPL8
Q7XPY1
Morphology
unknown but fine-mapped 9.3kb region
Oryza rufipogon
(species)
Oryza sativa
rice - (species)
OsLG1
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsPPKL1/qGL3
Grain size
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Zhang X; Wang J; Huang J ; et al. (2012)
Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield[...]
GP00000812
qLTG-3-1
B3IWI0
Morphology
Asp364Glu
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsPPKL1/qGL3
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsSPL13
Grain size
Cis-regulatory,
Insertion
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Domesticated
Association Mapping
Si L; Chen J; Huang X ; et al. (2016)
OsSPL13 controls grain size in cultivated rice.
GP00001572
SPL13
Q6Z461
Morphology
a CACTTC tandem repeat sequence in the 5' UTR is causing reduced expression
Oryza sativa
rice - (species)
Oryza sativa Japonica Group
Japanese rice - (no rank) D
OsSPL13
Oryza sativa Japonica Group
Japanese rice - (no rank)
Published - Accepted by Curator
OsSPL14 / WFP
Grain yield
Cis-regulatory,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Jiao Y; Wang Y; Xue D ; et al. (2010)
Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice.
1 Additional References
GP00000813
IPA1
D8WJ58
Morphology
Point mutation resulting in altered binding of a micro-RNA
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsSPL14 / WFP
Oryza sativa
rice - (species)
Published - Accepted by Curator
OsSPL16
Grain size
Grain shape
Cis-regulatory,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang S; Wu K; Yuan Q ; et al. (2012)
Control of grain size, shape and quality by OsSPL16 in rice.
1 Additional References
GP00000814
SPL16
L0AP48
Morphology
Morphology
Promoter variation
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
OsSPL16
Oryza sativa
rice - (species)
Published - Accepted by Curator
OVATE
Fruit shape
Coding,
SNP
N
Solanum lycopersicum
tomato - (species)
Domesticated
Linkage Mapping
Liu J; Van Eck J; Cong B ; et al. (2002)
A new class of regulatory genes underlying the cause of pear-shaped tomato fruit.
GP00000815
Q8GSM4
Morphology
V164* caused by G>T; which leads to a 75-aa truncation in the C terminus of the predicted protein N
Solanum lycopersicum
tomato - (species)
Solanum lycopersicum
tomato - (species)
OVATE
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
PABPN1
Recombination rate
Unknown,
Unknown
Bos taurus
cattle - (species)
Domesticated
Association Mapping
Ma L; O'Connell JR; VanRaden PM ; et al. (2015)
Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.
GP00001660
PABPN1
Q28165
Physiology
On chromosome 10. Associated SNP located dowstream of PABPN1
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
PABPN1
Bos taurus
cattle - (species)
Published - Accepted by Curator
Pax3
Coloration (white-spotting ; leucism)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Linkage Mapping
Hauswirth R; Haase B; Blatter M ; et al. (2012)
Mutations in MITF and PAX3 cause "splashed white" and other white spotting phenotypes in horses.
GP00002252
PAX3
P23760
Morphology
c.209G>A p.C70Y
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Pax3
Equus caballus
horse - (species)
Published - Accepted by Curator
Pax3
Coloration (white-spotting ; leucism)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Hauswirth R; Jude R; Haase B ; et al. (2013)
Novel variants in the KIT and PAX3 genes in horses with white-spotted coat colour phenotypes.
GP00002253
PAX3
P23760
Morphology
c.95C>G p.Pro32Arg
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
Pax3
Equus caballus
horse - (species)
Published - Accepted by Curator
PDSS2
Feather
Cis-regulatory,
SNP
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Feng C; Gao Y; Dorshorst B ; et al. (2014)
A cis-regulatory mutation of PDSS2 causes silky-feather in chickens.
GP00002254
Q86YH6NULL
Morphology
Only variant explaining homozygous phenotype is c.-103C>G and shown to reduce PDSS2 promoter activity in vitro
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
PDSS2
Gallus gallus
chicken - (species)
Published - Accepted by Curator
pericarp color1 (P1)
Coloration (seed)
Cis-regulatory,
Insertion
Zea mays
(species) D
Domesticated
Linkage Mapping
Lechelt C; Peterson T; Laird A ; et al. (1989)
Isolation and molecular analysis of the maize P locus.
GP00000859
P1
O24579
Morphology
insertion of transposable element Ac within a large intron; affecting transcripts. The five transcripts found in P-RR plants are absent in P-VV. A chimeric transcript containing part of Ac sequence is found.
Zea mays
(species)
Zea mays
(species) D
pericarp color1 (P1)
Zea mays
(species)
Published - Accepted by Curator
PG
Fruit ripening
Coding,
Deletion
N
Capsicum annuum
(species) D
Domesticated
Candidate Gene
Kim S; Park M; Yeom SI ; et al. (2014)
Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum speci[...]
GP00001448
PG
B9VRK6
Physiology
a partial deletion of about 90aa in the C-terminal region N
Solanum lycopersicum
tomato - (species)
Capsicum annuum
(species) D
PG
Capsicum annuum
(species)
Published - Accepted by Curator
PG
Fruit ripening
Coding,
SNP
N
Capsicum chinense
(species) D
Domesticated
Candidate Gene
Kim S; Park M; Yeom SI ; et al. (2014)
Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum speci[...]
GP00001449
PG
B9VRK6
Physiology
a point mutation in the 3' splice acceptor site of intron VIII generates a premature stop codon N
Solanum lycopersicum
tomato - (species)
Capsicum chinense
(species) D
PG
Capsicum chinense
(species)
Published - Accepted by Curator
PH4/GmMYB-G20-1
Coloration (flowers)
Coding,
SNP
N
Glycine max
soybean - (species)
Domesticated
Linkage Mapping
Takahashi R; Benitez ER; Oyoo ME ; et al. (2011 Jul-Aug)
Nonsense mutation of an MYB transcription factor is associated with purple-blue flower color in soyb[...]
GP00000862
PH4
Q2TCH0
Morphology
Substitution creating premature Stop (codon 158) N
Glycine max
soybean - (species)
Glycine max
soybean - (species)
PH4/GmMYB-G20-1
Glycine max
soybean - (species)
Published - Accepted by Curator
PHO84
Xenobiotic resistance
Coding,
SNP
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Perlstein EO; Ruderfer DM; Roberts DC ; et al. (2007)
Genetic basis of individual differences in the response to small-molecule drugs in yeast.
GP00000865
PHO84
P25297
Physiology
L259P
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
PHO84
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
phytochrome A (PHYA)
Light sensitivity
High-altitude adaptation
Coding,
Insertion
N
Glycine max
soybean - (species) D
Domesticated
Candidate Gene
Liu B; Kanazawa A; Matsumura H ; et al. (2008)
Genetic redundancy in soybean photoresponses associated with duplication of the phytochrome A gene.
1 Additional References
GP00002104
PHYA
P14712
Physiology
Physiology
insertion of a retrotransposon in exon 1 - The transposable element is SORE-1 = a novel Ty1/copia-like retrotransposon in soybean N
Glycine max
soybean - (species)
Glycine max
soybean - (species) D
phytochrome A (PHYA)
Glycine max
soybean - (species)
Published - Accepted by Curator
phytochrome A-associated F-box protein
Circadian rhythm (phase)
Coding,
Deletion
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Müller NA; Wijnen CL; Srinivasan A ; et al. (2016)
Domestication selected for deceleration of the circadian clock in cultivated tomato.
GP00001287
101247753
K4CV85
Physiology
3bp deletion in CDS causing a 'K (lysine) loss in the highly conserved C terminus of EID1
Solanum pimpinellifolium
(species)
Solanum lycopersicum
tomato - (species) D
phytochrome A-associated F-box protein
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
phytochrome B (PHYB)
Light sensitivity
Coding,
Deletion
Sorghum bicolor
sorghum - (species) D
Domesticated
Linkage Mapping
Childs KL; Miller FR; Cordonnier-Pratt MM ; et al. (1997)
The sorghum photoperiod sensitivity gene, Ma3, encodes a phytochrome B.
GP00000872
PHYB
P14713
Physiology
1bp deletion 30bp upstream of the stop codon
Sorghum bicolor
sorghum - (species)
Sorghum bicolor
sorghum - (species) D
phytochrome B (PHYB)
Sorghum bicolor
sorghum - (species)
Published - Accepted by Curator
phytoene synthase
Carotenoid content (seed)
Unknown,
Unknown
Zea mays
(species)
Domesticated
Linkage Mapping
Palaisa KA; Morgante M; Williams M ; et al. (2003)
Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene sy[...]
1 Additional References
GP00000875
PSY1
P49085
Physiology
Not identified
Zea mays
(species)
Zea mays
(species)
phytoene synthase
Zea mays
(species)
Published - Accepted by Curator
phytoene synthase
Carotenoid content (fruit)
Coding,
Insertion
N
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Fray RG; Grierson D (1993)
Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequen[...]
1 Additional References
GP00001718
PSY1
P49085
Physiology
insertion of a Rider transposable element within the coding region N
Solanum lycopersicum
tomato - (species)
Solanum lycopersicum
tomato - (species) D
phytoene synthase
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
phytoene synthase
Carotenoid content (fruit)
Coding,
Indel
N
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Fray RG; Grierson D (1993)
Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequen[...]
1 Additional References
GP00001719
PSY1
P49085
Physiology
r y cDNA was found to be mutated at its 3' end, lacking the last 237 bases of PSY1 coding sequence and containing 185 nucleotides of an unrelated sequence in its place N
Solanum lycopersicum
tomato - (species)
Solanum lycopersicum
tomato - (species) D
phytoene synthase
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
Pi-ta
Pathogen resistance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Bryan GT; Wu KS; Farrall L ; et al. (2000)
tA single amino acid difference distinguishes resistant and susceptible alleles of the rice blast re[...]
2 Additional References
GP00000876
Pi-ta
C9E6G5
Physiology
Ala918Ser
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pi-ta
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pi2 (Nbs4-Pi2)
Pathogen resistance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Zhou B; Qu S; Liu G ; et al. (2006)
The eight amino-acid differences within three leucine-rich repeats between Pi2 and Piz-t resistance [...]
GP00000877
PI2
M1EC06
Physiology
eight amino acid changes - exact causing change(s) unknown
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pi2 (Nbs4-Pi2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pi36
Pathogen resistance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Liu X; Lin F; Wang L ; et al. (2007)
The in silico map-based cloning of Pi36, a rice coiled-coil nucleotide-binding site leucine-rich rep[...]
GP00000878
Pi36
D5J6W0
Physiology
Asp590Ser
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pi36
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pi37
Pathogen resistance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Lin F; Chen S; Que Z ; et al. (2007)
The blast resistance gene Pi37 encodes a nucleotide binding site leucine-rich repeat protein and is [...]
GP00000879
Pi37
Q06AJ9
Physiology
V239A and I247M are the only amino acid substitutions found in all tested resistant strains- the effect of each individual amino acid change has not been tested
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pi37
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pi5-1 + Pi5-2 cluster
Pathogen resistance
Coding,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Lee SK; Song MY; Seo YS ; et al. (2009)
Rice Pi5-mediated resistance to Magnaporthe oryzae requires the presence of two coiled-coil-nucleoti[...]
GP00000880
Pi5-1
C3SBK3
Physiology
In genetic transformation experiments of a susceptible rice cultivar neither the Pi5-1 nor the Pi5-2 gene was found to confer resistance to M. oryzae. In contrast transgenic rice plants expressing both of these genes (generated by crossing transgenic lines carrying each gene individually) conferred Pi5-mediated resistance to M. oryzae
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pi5-1 + Pi5-2 cluster
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pi9 (= Nbs2-Pi9)
Pathogen resistance
Coding,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Qu S; Liu G; Zhou B ; et al. (2006)
The broad-spectrum blast resistance gene Pi9 encodes a nucleotide-binding site-leucine-rich repeat p[...]
GP00000881
Pi9
Q1WGB0
Physiology
Coding variation; necessary for resistance in completementation assay
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pi9 (= Nbs2-Pi9)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pib
Pathogen resistance
Unknown,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang ZX; Yano M; Yamanouchi U ; et al. (1999)
The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat cla[...]
GP00000882
Pi-b
Q9SSY0
Physiology
unknown
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pib
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pid3
Pathogen resistance
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Chen J; Shi Y; Liu W ; et al. (2011)
A Pid3 allele from rice cultivar Gumei2 confers resistance to Magnaporthe oryzae.
GP00000883
Pid3
C0LMX9
Physiology
1bp deletion resulting in truncated protein N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Pid3
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pikm1-TS + Pikm2-TS cluster
Pathogen resistance
Coding,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Ashikawa I; Hayashi N; Yamane H ; et al. (2008)
Two adjacent nucleotide-binding site-leucine-rich repeat class genes are required to confer Pikm-spe[...]
1 Additional References
GP00000884
PIKM1-TS
B5UBC1
Physiology
Coding variation in both genes; with alleles of both genes necessary for resistance in completementation assays
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Pikm1-TS + Pikm2-TS cluster
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pit
Pathogen resistance (rice blast disease; fungal pathogen; Magnaporthe grisea)
Cis-regulatory,
Insertion
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Hayashi K; Yoshida H (2009)
Refunctionalization of the ancient rice blast disease resistance gene Pit by the recruitment of a re[...]
GP00002052
Pit
B9A1G4
Physiology
insertion of a 5.5-kb LTR retrotransposon Renovator upstream of the gene (256‐bp upstream of the predicted start codon for NBSt2K59; in the same orientation as the gene)
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Pit
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pitx1
Limb Identity (feathered feet)
Cis-regulatory,
Deletion
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Kronenberg Z; Infante CR ; et al. (2016)
Molecular shifts in limb identity underlie development of feathered feet in two domestic avian speci[...]
GP00000885
PITX1
P56673
Morphology
44kb deletion
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
Pitx1
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
Piz-t
Pathogen resistance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Zhou B; Qu S; Liu G ; et al. (2006)
The eight amino-acid differences within three leucine-rich repeats between Pi2 and Piz-t resistance [...]
GP00000895
Piz-t
Q0H213
Physiology
Coding variation in the LRR domain
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Piz-t
Oryza sativa
rice - (species)
Published - Accepted by Curator
Pl6
Pathogen resistance
Coding,
Unknown
Helianthus annuus
common sunflower - (species) D
Domesticated
Linkage Mapping
Franchel J; Bouzidi MF; Bronner G ; et al. (2013)
Positional cloning of a candidate gene for resistance to the sunflower downy mildew, Plasmopara hals[...]
GP00000896
F8R6K4
Physiology
unknown ; cluster of several R-protein coding genes; of which only one is expressed
Helianthus annuus
common sunflower - (species)
Helianthus annuus
common sunflower - (species) D
Pl6
Helianthus annuus
common sunflower - (species)
Published - Accepted by Curator
PLAG1
Body size (height; weight)
Cis-regulatory,
Insertion
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Karim L; Takeda H; Lin L ; et al. (2011)
Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine statur[...]
GP00001569
PLAG1
E1BEA5
Morphology
a (CCG)n trinucleotide repeat with 9> 11 copies and a SNP A>G immediately upstream of PLAG1 transcriptional start site
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
PLAG1
Bos taurus
cattle - (species)
Published - Accepted by Curator
PMEL17
Coloration (feathers)
Coding,
Deletion
Gallus gallus
chicken - (species) D
Domesticated
Candidate Gene
Kerje S; Sharma P; Gunnarsson U ; et al. (2004)
The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion p[...]
GP00000911
PMEL
Q98917
Morphology
deletion of amino acids 731-735
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
PMEL17
Gallus gallus
chicken - (species)
Published - Accepted by Curator
PMEL17
Coloration (feathers)
Coding,
Deletion
Gallus gallus
chicken - (species) D
Domesticated
Candidate Gene
Kerje S; Sharma P; Gunnarsson U ; et al. (2004)
The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion p[...]
GP00000912
PMEL
Q98917
Morphology
deletion of amino acids 280-284
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
PMEL17
Gallus gallus
chicken - (species)
Published - Accepted by Curator
PMEL17
Coloration (feathers)
Coding,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Kerje S; Sharma P; Gunnarsson U ; et al. (2004)
The Dominant white, Dun and Smoky color variants in chicken are associated with insertion/deletion p[...]
GP00000913
PMEL
Q98917
Morphology
insertion of amino acid 723-725 due to a 9bp-insert in exon 10
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
PMEL17
Gallus gallus
chicken - (species)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Coding,
Deletion
Bos grunniens
domestic yak - (species) D
Domesticated
Candidate Gene
Zhang MQ; Xu X; Luo SJ (2014)
The genetics of brown coat color and white spotting in domestic yaks (Bos grunniens).
GP00001365
PMEL
P40967
Morphology
c.50_52del p.Leu18del in signal peptide
Bos grunniens
domestic yak - (species)
Bos grunniens
domestic yak - (species) D
PMEL17
Bos grunniens
domestic yak - (species)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Gutiérrez-Gil B; Wiener P; Williams JL (2007)
Genetic effects on coat colour in cattle: dilution of eumelanin and phaeomelanin pigments in an F2-B[...]
GP00002027
PMEL
Q06154
Morphology
g.57669926G>A c.64G>A p.Gly22Arg
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
PMEL17
Bos taurus
cattle - (species)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Coding,
Deletion
Bos taurus
cattle - (species) D
Bos grunniens
domestic yak - (species) D
Domesticated
Candidate Gene
Jolly RD; Wills JL; Kenny JE ; et al. (2008)
Coat-colour dilution and hypotrichosis in Hereford crossbred calves.
GP00002028
PMEL
Q06154
Morphology
3bp deletion - g.57669913_57669915delTTC - c.50_52delTTC - p.Leu19del
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Bos grunniens
domestic yak - (species) D
PMEL17
Bos taurus
cattle - (species)
Bos grunniens
domestic yak - (species)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Clark LA; Wahl JM; Rees CA ; et al. (2006)
Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog.
GP00002072
Pmel
Q60696
Morphology
due to a short interspersed element (SINE) insertion at the intron 10/exon 11 boundary. The SINE segregates with the merle phenotype in multiple breeds (Collie, Border Collie, Australian Shepherd, Cardigan Welsh Corgi, Dachshund, and Great Dane) and is absent from dogs representing breeds that do not have merle patterning. All examined harlequin Great Danes harbored the insertion in either a heterozygous or homozygous state.
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
PMEL17
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Coding,
Insertion
Mus musculus
house mouse - (species) D
Domesticated
Linkage Mapping
Kwon BS; Halaban R; Ponnazhagan S ; et al. (1995)
Mouse silver mutation is caused by a single base insertion in the putative cytoplasmic domain of Pme[...]
GP00002101
Pmel
Q60696
Morphology
single nucleotide (A) insertion in the putative cytoplasmic tail of the si/si Pmel 17 cDNA clone. This insertion is predicted to alter the last 24 amino acids at the C-terminus. Also predicted is the extension of the Pmel 17 protein by 12 residues because a new termination signal is created downstream from the wild-type reading frame. The silver pmel 17 protein has a major defect at the carboxyl terminus.
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species) D
PMEL17
Mus musculus
house mouse - (species)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Langevin M; Synkova H; Jancuskova T ; et al. (2018)
Merle phenotypes in dogs - SILV SINE insertions from Mc to Mh.
1 Additional References
GP00002266
Pmel
Q60696
Morphology
Allele of the Merle SINE insertaiion : Mc (208-230bp)
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
PMEL17
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Langevin M; Synkova H; Jancuskova T ; et al. (2018)
Merle phenotypes in dogs - SILV SINE insertions from Mc to Mh.
1 Additional References
GP00002267
Pmel
Q60696
Morphology
Allele of the Merle SINE insertion : Mc+ (231-245bp)
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
PMEL17
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Langevin M; Synkova H; Jancuskova T ; et al. (2018)
Merle phenotypes in dogs - SILV SINE insertions from Mc to Mh.
1 Additional References
GP00002268
Pmel
Q60696
Morphology
Allele of the Merle SINE insertion : Ma (247-254bp)
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
PMEL17
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Langevin M; Synkova H; Jancuskova T ; et al. (2018)
Merle phenotypes in dogs - SILV SINE insertions from Mc to Mh.
1 Additional References
GP00002269
Pmel
Q60696
Morphology
Allele of the Merle SINE insertion : Ma+ (255-264bp)
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
PMEL17
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Langevin M; Synkova H; Jancuskova T ; et al. (2018)
Merle phenotypes in dogs - SILV SINE insertions from Mc to Mh.
1 Additional References
GP00002270
Pmel
Q60696
Morphology
Allele of the Merle SINE insertion : Mh (269-277bp)
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
PMEL17
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
PMEL17
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Brunberg E; Andersson L; Cothran G ; et al. (2006)
A missense mutation in PMEL17 is associated with the Silver coat color in the horse.
4 Additional References
GP00002271
Pmel
Q60696
Morphology
g.73665304C>T p.R625C
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
PMEL17
Equus caballus
horse - (species)
Published - Accepted by Curator
PMR1
Metal tolerance (manganese)
Coding,
SNP
Saccharomyces cerevisiae
baker's yeast - (species) D
Domesticated
Linkage Mapping
Sadhu MJ; Bloom JS; Day L ; et al. (2016)
CRISPR-directed mitotic recombination enables genetic mapping without crosses.
GP00000914
PMR1
P13586
Physiology
Leu548Phe
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species) D
PMR1
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
POLLED locus
Horns absence
Cis-regulatory,
Indel
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Medugorac I; Seichter D; Graf A ; et al. (2012)
Bovine polledness--an autosomal dominant trait with allelic heterogeneity.
2 Additional References
GP00000916
Morphology
complex 202-bp insertion-deletion in a non-coding region resulting in a long non-coding RNA (lncRNA) ectopic expression
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
POLLED locus
Bos taurus
cattle - (species)
Published - Accepted by Curator
POLLED locus
Horns absence
Cis-regulatory,
Insertion
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Medugorac I; Seichter D; Graf A ; et al. (2012)
Bovine polledness--an autosomal dominant trait with allelic heterogeneity.
3 Additional References
GP00002029
Morphology
a 80kb duplication is the "single causal mutation" in Holstein-Friesian cattle complex
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
POLLED locus
Bos taurus
cattle - (species)
Published - Accepted by Curator
POLLED locus
Horns absence
Cis-regulatory,
Complex Change
Bos taurus
cattle - (species) D
Bos grunniens
domestic yak - (species) D
Domesticated
Association Mapping
Medugorac I; Graf A; Grohs C ; et al. (2017)
Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mo[...]
GP00002030
Morphology
a complex 219-bp duplication–insertion (P219ID) beginning at 1;976;128 bp and a 7-bp deletion and 6-bp insertion (P1ID) located 621 bp upstream of this position. This rearrangement results in duplication of an 11-bp motif (5′-AAAGAAGCAAA-3′) that is entirely conserved among Bovidae and that is also duplicated in the 80-kb duplication responsible for Friesian polledness.
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Bos grunniens
domestic yak - (species) D
POLLED locus
Bos taurus
cattle - (species)
Bos grunniens
domestic yak - (species)
Published - Accepted by Curator
POLLED locus
Horns absence
Cis-regulatory,
Insertion
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Utsunomiya YT; Torrecilha RBP; Milanesi M ; et al. (2019)
Hornless Nellore cattle (Bos indicus) carrying a novel 110 kbp duplication variant of the polled loc[...]
GP00002031
Morphology
duplication of the region BTA1: 1;893;790–2;004;553 (about 110 kb)
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
POLLED locus
Bos taurus
cattle - (species)
Published - Accepted by Curator
Potassium channel subfamily K
Fin morphology (skeleton; dorsal fin; caudal fin; tail; paired fin)
Coding,
SNP
N
Carassius auratus
goldfish - (species) D
Domesticated
Association Mapping
Kon T; Omori Y; Fukuta K ; et al. (2020)
The Genetic Basis of Morphological Diversity in Domesticated Goldfish.
GP00002348
KCNK5
O95279
Morphology
Substitution of a hydrophobic amino acid (valine) with a hydrophilic amino acid (glutamic acid) appears to cause a critical alteration of channel gating. In total there are five amino acid substitutions or deletions in kcnk5bS in goldfish with the long-tail phenotype. N
Carassius auratus
goldfish - (species)
Carassius auratus
goldfish - (species) D
Potassium channel subfamily K
Carassius auratus
goldfish - (species)
Published - Accepted by Curator
PPAR-delta
Ear size
Skin aspect
Coding,
SNP
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Ren J; Duan Y; Qiao R ; et al. (2011)
A missense mutation in PPARD causes a major QTL effect on ear size in pigs.
GP00000919
PPARD
Q03181
Morphology
Morphology
G32E
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
PPAR-delta
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
PpeGID1c
Plant size (dwarfism)
Coding,
SNP
N
Prunus persica
peach - (species) D
Domesticated
Linkage Mapping
Hollender CA; Hadiarto T; Srinivasan C ; et al. (2016)
A brachytic dwarfism trait (dw) in peach trees is caused by a nonsense mutation within the gibberell[...]
GP00000920
GID1C
Q940G6
Morphology
Trp162* (TGG>TAG) N
Prunus persica
peach - (species)
Prunus persica
peach - (species) D
PpeGID1c
Prunus persica
peach - (species)
Published - Accepted by Curator
PRDM9
Recombination rate (male)
Coding,
Deletion
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Sandor C; Li W; Coppieters W ; et al. (2012)
Genetic variants in REC8, RNF212, and PRDM9 influence male recombination in cattle.
GP00001640
PRDM9
A6QNW2
Physiology
variation in the C-terminal tandem array of Cys2His2 zinc-finger domains: 22 domains > 20 domains decreasing 6-fold Genome wide hot window usage in Crossing Over
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
PRDM9
Bos taurus
cattle - (species)
Published - Accepted by Curator
PRDM9
Recombination rate (male)
Coding,
SNP
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Sandor C; Li W; Coppieters W ; et al. (2012)
Genetic variants in REC8, RNF212, and PRDM9 influence male recombination in cattle.
GP00001641
PRDM9
A6QNW2
Physiology
variation in the C-terminal tandem array of Cys2His2 zinc-finger domains: T68A p.I23K in domain 11 has a major effect. K allele decreasing 30-fold Genome wide hot window usage in Crossing Over compared to I allele
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
PRDM9
Bos taurus
cattle - (species)
Published - Accepted by Curator
PRDM9
Recombination rate (male)
Coding,
SNP
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Sandor C; Li W; Coppieters W ; et al. (2012)
Genetic variants in REC8, RNF212, and PRDM9 influence male recombination in cattle.
GP00001642
PRDM9
A6QNW2
Physiology
variation in the C-terminal tandem array of Cys2His2 zinc-finger domains: T20C p.A>Y sustitutions in domains 14. Y allele increasing 6-fold Genome wide hot window usage in Crossing Over
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
PRDM9
Bos taurus
cattle - (species)
Published - Accepted by Curator
PRKG2
Body size (dwarfism)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Koltes JE; Mishra BP; Kumar D ; et al. (2009)
A nonsense mutation in cGMP-dependent type II protein kinase (PRKG2) causes dwarfism in American Ang[...]
GP00002273
PRKG2
Q13237
Morphology
c.1573C>T p.R525* N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
PRKG2
Bos taurus
cattle - (species)
Published - Accepted by Curator
PRKG2
Body size (dwarfism)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Koltes JE; Mishra BP; Kumar D ; et al. (2009)
A nonsense mutation in cGMP-dependent type II protein kinase (PRKG2) causes dwarfism in American Ang[...]
GP00002274
PRKG2
Q13237
Morphology
c.2032C>T p.R678* N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
PRKG2
Bos taurus
cattle - (species)
Published - Accepted by Curator
PROG1
Plant architecture
Unknown,
Unknown
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Tan L; Li X; Liu F ; et al. (2008)
Control of a key transition from prostrate to erect growth in rice domestication.
2 Additional References
GP00000925
PROG1
Q69NY0
Morphology
Various
Oryza rufipogon
(species)
Oryza sativa
rice - (species)
PROG1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Prolactin
Hair length (long)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Littlejohn MD; Henty KM; Tiplady K ; et al. (2014)
Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle.
GP00002032
PRL
P01239
Morphology
g.35105313A>C - c.661A>C - p.C221G
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Prolactin
Bos taurus
cattle - (species)
Published - Accepted by Curator
Prolactin
Hair length (short)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Littlejohn MD; Henty KM; Tiplady K ; et al. (2014)
Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle.
GP00002033
PRL
P01239
Morphology
1-bp deletion in exon 10 that introduces a premature stop codon (p.Leu462*) and loss of 120 C-terminal amino acids from the long isoform of the receptor (ss1067289408; chr20:39136558GC>G) N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Prolactin
Bos taurus
cattle - (species)
Published - Accepted by Curator
Prolactin receptor
Milk yield
Coding,
SNP
Bos taurus
cattle - (species)
Domesticated
Candidate Gene
Viitala S; Szyda J; Blott S ; et al. (2006)
The role of the bovine growth hormone receptor and prolactin receptor genes in milk, fat and protein[...]
GP00000927
PRLR
P16471
Physiology
Ser18Asn
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
Prolactin receptor
Bos taurus
cattle - (species)
Published - Accepted by Curator
Prolactin receptor
Feather (slow-feathering ; delay)
Other,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Elferink MG; Vallée AA; Jungerius AP ; et al. (2008)
Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken.
1 Additional References
GP00002280
PRLR
P16471
Morphology
tandem duplication of 176324 basepairs resulting in a partially duplicated PRLR (dPRLR) gene nearly identical to the original PRLR ; except for its lack of a 149-amino acid C-terminal tail - which may titrate PRL ligands and act as a dominant-negative receptor
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
Prolactin receptor
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Prolactin receptor
Feather (slow-feathering ; delay)
Coding,
Deletion
Meleagris gallopavo mexicana
(subspecies) D
Domesticated
Association Mapping
Derks MFL; Herrero-Medrano JM; Crooijmans RPMA ; et al. (2018)
Early and late feathering in turkey and chicken: same gene but different mutations.
GP00002281
PRLR
P16471
Morphology
g.9426018_9426022delTTGGT p.Glu726Aspfs*7 truncated PRLR protein that lacks 98 C-terminal AA ; this truncated PRLR protein is strikingly similar to the protein encoded by the slow feathering K allele in chicken
Meleagris gallopavo mexicana
(subspecies)
Meleagris gallopavo mexicana
(subspecies) D
Prolactin receptor
Meleagris gallopavo mexicana
(subspecies)
Published - Accepted by Curator
Prolactin receptor
Hair (slick ; short ; thermotolerance)
Thermoregulation (tolerance to warm climate)
Coding,
Deletion
N
Bos taurus
cattle - (species) D
Domesticated
Littlejohn MD; Henty KM; Tiplady K ; et al. (2014)
Functionally reciprocal mutations of the prolactin signalling pathway define hairy and slick cattle.
GP00002282
PRLR
P16471
Morphology
Physiology
g.39136559delC p.Leu462* N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Prolactin receptor
Bos taurus
cattle - (species)
Published - Accepted by Curator
Prolactin receptor
Hair (slick ; short)
Thermoregulation (tolerance to warm climate)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Porto-Neto LR; Bickhart DM; Landaeta-Hernandez AJ ; et al. (2018)
Convergent Evolution of Slick Coat in Cattle through Truncation Mutations in the Prolactin Receptor.
GP00002283
PRLR
P16471
Morphology
Physiology
g.39136571C>A p.Ser465* N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Prolactin receptor
Bos taurus
cattle - (species)
Published - Accepted by Curator
Prolactin receptor
Hair (slick ; short)
Thermoregulation (tolerance to warm climate)
Coding,
SNP
N
Bos taurus
cattle - (species) D
Domesticated
Porto-Neto LR; Bickhart DM; Landaeta-Hernandez AJ ; et al. (2018)
Convergent Evolution of Slick Coat in Cattle through Truncation Mutations in the Prolactin Receptor.
GP00002284
PRLR
P16471
Morphology
Physiology
g.39136666C>T p.Arg497* N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Prolactin receptor
Bos taurus
cattle - (species)
Published - Accepted by Curator
Prolactin receptor
Fertility
Cis-regulatory,
Insertion
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Linkage Mapping
Sironen A; Fischer D; Laiho A ; et al. (2014)
A recent L1 insertion within SPEF2 gene is associated with changes in PRLR expression in sow reprodu[...]
1 Additional References
GP00002339
PRLR
P16471
Physiology
L1 insertion in sperm-factor SPEF2 gene causes sperm defect but also downregulation of PRLR
Sus scrofa domesticus
domestic pig - (subspecies)
Sus scrofa domesticus
domestic pig - (subspecies) D
Prolactin receptor
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Prolactin releasing hormone receptor (Prlhr/GPR10)
Body size (weight)
Cis-regulatory,
Unknown
Mus musculus
house mouse - (species)
Domesticated
Association Mapping
Chan YF; Jones FC; McConnell E ; et al. (2012)
Parallel selection mapping using artificially selected mice reveals body weight control loci.
GP00000928
PRLHR
P49683
Physiology
unknown
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species)
Prolactin releasing hormone receptor (Prlhr/GPR10)
Mus musculus
house mouse - (species)
Published - Accepted by Curator
PRR37 pseudoresponse regulator protein 37
Flowering time
Coding,
Deletion
N
Sorghum bicolor
sorghum - (species) D
Domesticated
Linkage Mapping
Murphy RL; Klein RR; Morishige DT ; et al. (2011)
Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photop[...]
GP00000930
PRR37
Q0D3B6
Physiology
1bp deletion resulting in frameshift N
Sorghum bicolor
sorghum - (species)
Sorghum bicolor
sorghum - (species) D
PRR37 pseudoresponse regulator protein 37
Sorghum bicolor
sorghum - (species)
Published - Accepted by Curator
PRR37 pseudoresponse regulator protein 37
Flowering time
2 Mutations:
Coding
SNP
N
Sorghum bicolor
sorghum - (species)
Domesticated
Linkage Mapping
Murphy RL; Klein RR; Morishige DT ; et al. (2011)
Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photop[...]
GP00000931
PRR37
Q0D3B6
Physiology
2 mutations
Sorghum bicolor
sorghum - (species)
Sorghum bicolor
sorghum - (species)
PRR37 pseudoresponse regulator protein 37
Sorghum bicolor
sorghum - (species)
Published - Accepted by Curator
PRR37 pseudoresponse regulator protein 37
Flowering time
Coding,
SNP
Sorghum bicolor
sorghum - (species)
Domesticated
Linkage Mapping
Murphy RL; Klein RR; Morishige DT ; et al. (2011)
Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photop[...]
GP00000932
PRR37
Q0D3B6
Physiology
K162N
Sorghum bicolor
sorghum - (species)
Sorghum bicolor
sorghum - (species)
PRR37 pseudoresponse regulator protein 37
Sorghum bicolor
sorghum - (species)
Published - Accepted by Curator
PRR37 pseudoresponse regulator protein 37
Flowering time (heading date)
Coding,
SNP
N
Oryza sativa Japonica Group
Japanese rice - (no rank) D
Domesticated
Linkage Mapping
Koo BH; Yoo SC; Park JW ; et al. (2013)
Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide ra[...]
GP00001632
PRR37
Q0D3B6
Physiology
Nonfunctional allele PRR37-2a: L710P missense mutation in the CONSTANS-Co-like and TOC1 domain of the protein N
Oryza sativa
rice - (species)
Oryza sativa Japonica Group
Japanese rice - (no rank) D
PRR37 pseudoresponse regulator protein 37
Oryza sativa Japonica Group
Japanese rice - (no rank)
Published - Accepted by Curator
PRR37 pseudoresponse regulator protein 37
Flowering time (heading date)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Koo BH; Yoo SC; Park JW ; et al. (2013)
Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide ra[...]
GP00001633
PRR37
Q0D3B6
Physiology
Nonfunctional allele PRR37-1a: a 8-bp deletion at position 1515 leading to frameshift N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
PRR37 pseudoresponse regulator protein 37
Oryza sativa
rice - (species)
Published - Accepted by Curator
PRR37 pseudoresponse regulator protein 37
Flowering time (heading date)
Coding,
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Koo BH; Yoo SC; Park JW ; et al. (2013)
Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide ra[...]
GP00001634
PRR37
Q0D3B6
Physiology
Nonfunctional allele PRR37-1b: Y704H N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
PRR37 pseudoresponse regulator protein 37
Oryza sativa
rice - (species)
Published - Accepted by Curator
PRR37 pseudoresponse regulator protein 37
Flowering time (heading date)
Coding,
SNP
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Koo BH; Yoo SC; Park JW ; et al. (2013)
Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide ra[...]
GP00001635
PRR37
Q0D3B6
Physiology
Nonfunctional allele PRR37-1c: a premature stop Q705* N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
PRR37 pseudoresponse regulator protein 37
Oryza sativa
rice - (species)
Published - Accepted by Curator
PRR37-like Photoperiod-H1 (Ppd-H1)
Flowering time
Unknown,
Unknown
Hordeum vulgare
(species)
Domesticated
Linkage Mapping
Turner A; Beales J; Faure S ; et al. (2005)
The pseudo-response regulator Ppd-H1 provides adaptation to photoperiod in barley.
1 Additional References
GP00000933
PRR37
Q0D3B6
Physiology
unknown
Hordeum vulgare
(species)
Hordeum vulgare
(species)
PRR37-like Photoperiod-H1 (Ppd-H1)
Hordeum vulgare
(species)
Published - Accepted by Curator
PsbHLH = A
Coloration (flowers)
Coding,
SNP
N
Pisum sativum
pea - (species)
Domesticated
Linkage Mapping
Hellens RP; Moreau C; Lin-Wang K ; et al. (2010)
Identification of Mendel's white flower character.
GP00000935
BHLH
E3SXU4
Morphology
Splice site mutation: a simple G to A transition in a splice donor site that leads to a mis-spliced mRNA with a premature stop codon N
Pisum sativum
pea - (species)
Pisum sativum
pea - (species)
PsbHLH = A
Pisum sativum
pea - (species)
Published - Accepted by Curator
PSMB7
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies)
Domesticated
Linkage Mapping
Clark LA; Tsai KL; Starr AN ; et al. (2011)
A missense mutation in the 20S proteasome β2 subunit of Great Danes having harlequin coat patterning[...]
GP00000936
Psmb7
P70195
Morphology
c.146T>G p.V6G
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies)
PSMB7
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Pto
Pathogen resistance
Unknown,
Unknown
Solanum lycopersicum
tomato - (species)
Domesticated
Linkage Mapping
Martin GB; Brommonschenkel SH; Chunwongse J ; et al. (1993)
Map-based cloning of a protein kinase gene conferring disease resistance in tomato.
GP00000937
pto
P93215
Physiology
Not identified
Solanum lycopersicum
tomato - (species)
Solanum lycopersicum
tomato - (species)
Pto
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
Purple (Pr)
Plant color
Cis-regulatory,
Unknown
Brassica oleracea var. botrytis
(varietas)
Domesticated
Linkage Mapping
Chiu LW; Zhou X; Burke S ; et al. (2010)
The purple cauliflower arises from activation of a MYB transcription factor.
GP00000939
MYB2
E5D8F5
Morphology
unknown
Brassica oleracea
wild cabbage - (species)
Brassica oleracea var. botrytis
(varietas)
Purple (Pr)
Brassica oleracea var. botrytis
(varietas)
Published - Accepted by Curator
Q = wheat AP2-like (WAP2)
Inflorescence morphology
Spike morphology
Coding,
SNP
Triticum turgidum
(species)
Domesticated
Linkage Mapping
Simons KJ; Fellers JP; Trick HN ; et al. (2006)
Molecular characterization of the major wheat domestication gene Q.
GP00000940
WANT1
C1PH82
Morphology
Morphology
V329I
Triticum turgidum
(species)
Triticum turgidum
(species)
Q = wheat AP2-like (WAP2)
Triticum turgidum
(species)
Published - Accepted by Curator
qPE9-1
Plant architecture
Inflorescence architecture
Coding,
Indel
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Zhou Y; Zhu J; Li Z ; et al. (2009)
Deletion in a quantitative trait gene qPE9-1 associated with panicle erectness improves plant archit[...]
GP00000941
PAY1
B8Y995
Morphology
Morphology
637-bp deletion and 12-bp insertion resulting in truncated protein N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
qPE9-1
Oryza sativa
rice - (species)
Published - Accepted by Curator
qSH1
Seed shattering
Cis-regulatory,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Konishi S; Izawa T; Lin SY ; et al. (2006)
An SNP caused loss of seed shattering during rice domestication.
GP00000942
qSH1
Q941S9
Physiology
1bp change
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
qSH1
Oryza sativa
rice - (species)
Published - Accepted by Curator
qSW5
Grain size
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Shomura A; Izawa T; Ebana K ; et al. (2008)
Deletion in a gene associated with grain size increased yields during rice domestication.
1 Additional References
GP00000944
qSW5
F8SPD1
Morphology
1212bp deletion N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
qSW5
Oryza sativa
rice - (species)
Published - Accepted by Curator
R-spondin-2 (RSPO2)
Hair length (moustache / eyebrows)
Cis-regulatory,
Insertion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Cadieu E; Neff MW; Quignon P ; et al. (2009)
Coat variation in the domestic dog is governed by variants in three genes.
GP00000945
Rspo2
Q8BFU0
Morphology
a 167bp insertion within the 3'UTR at position which leads to a threefold increase in transcription of RSPO2 in muzzle skin of dogs with furnishings
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
R-spondin-2 (RSPO2)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
R/glyma09g36983
Coloration (seeds)
Coding,
SNP
N
Glycine max
soybean - (species)
Domesticated
Linkage Mapping
Gillman JD; Tetlow A; Lee JD ; et al. (2011)
Loss-of-function mutations affecting a specific Glycine max R2R3 MYB transcription factor result in [...]
1 Additional References
GP00000946
100780023
K7LFP2
Morphology
C377- creating premature Stop N
Glycine max
soybean - (species)
Glycine max
soybean - (species)
R/glyma09g36983
Glycine max
soybean - (species)
Published - Accepted by Curator
r1 colored1
Coloration (seeds)
Unknown,
Insertion
Zea mays
(species) D
Domesticated
Linkage Mapping
Hanson MA; Gaut BS; Stec AO ; et al. (1996)
Evolution of anthocyanin biosynthesis in maize kernels: the role of regulatory and enzymatic loci.
1 Additional References
GP00000947
Z138B04_Z333J11.11
Q8S483
Morphology
insertion of transposable element Ac
Zea mays
(species)
Zea mays
(species) D
r1 colored1
Zea mays
(species)
Published - Accepted by Curator
R2R3 MYB transcription factor
Trichome density (leaf)
Unknown,
Unknown
Erythranthe guttata
spotted monkey flower - (species)
Domesticated
Linkage Mapping
Hendrick MF; Finseth FR; Mathiasson ME ; et al. (2016)
The genetics of extreme microgeographic adaptation: an integrated approach identifies a major gene u[...]
GP00001598
PELAN
A0A060IEP7
Morphology
Unknown ; candidate indel in first intron and a nonsynonymous substitution (glutamine>lysine) in the 3rd exon
Erythranthe guttata
spotted monkey flower - (species)
Erythranthe guttata
spotted monkey flower - (species)
R2R3 MYB transcription factor
Erythranthe guttata
spotted monkey flower - (species)
Published - Accepted by Curator
RAD5
Xenobiotic resistance
Coding,
SNP
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Demogines A; Smith E; Kruglyak L ; et al. (2008)
Identification and dissection of a complex DNA repair sensitivity phenotype in Baker's yeast.
1 Additional References
GP00000950
RAD5
P32849
Physiology
I791S
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
RAD5
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
Rap2.7 (vgt1)
Flowering time
Cis-regulatory,
Unknown
Zea mays
(species)
Domesticated
Linkage Mapping
Salvi S; Sponza G; Morgante M ; et al. (2007)
Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in m[...]
1 Additional References
GP00000951
RAP2-7
Q9SK03
Physiology
2kb-sequence located 70kb upstream of the Vg1 transcription start site - insertion of a miniature transposon (MITE) belonging to the Tourist family
Zea mays
(species)
Zea mays
(species)
Rap2.7 (vgt1)
Zea mays
(species)
Published - Accepted by Curator
RAS2
Sporulation efficiency
Cis-regulatory,
Insertion
Saccharomyces cerevisiae
baker's yeast - (species) D
Domesticated
Linkage Mapping
Ben-Ari G; Zenvirth D; Sherman A ; et al. (2006)
Four linked genes participate in controlling sporulation efficiency in budding yeast.
GP00000956
RAS2
P01120
Physiology
1bp insertion in promoter
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species) D
RAS2
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
RB1
Body size (weight)
Body size (bone length)
Unknown,
Unknown
Gallus gallus
chicken - (species)
Domesticated
Linkage Mapping
Zhang H; Liu SH; Zhang Q ; et al. (2011)
Fine-mapping of quantitative trait loci for body weight and bone traits and positional cloning of th[...]
GP00000957
Morphology
Morphology
unknown
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
RB1
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Rc
Coloration (seed)
Coding,
SNP
N
Oryza glaberrima
African rice - (species)
Domesticated
Candidate Gene
Gross BL; Steffen FT; Olsen KM (2010)
The molecular basis of white pericarps in African domesticated rice: novel mutations at the Rc gene.
GP00000958
Rc
A7J5U6
Morphology
Premature stop codon in exon 7; Lys>* N
Oryza glaberrima
African rice - (species)
Oryza glaberrima
African rice - (species)
Rc
Oryza glaberrima
African rice - (species)
Published - Accepted by Curator
Rc
Coloration (seed)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Sweeney MT; Thomson MJ; Cho YG ; et al. (2007)
Global dissemination of a single mutation conferring white pericarp in rice.
GP00000959
Rc
A7J5U6
Morphology
14bp deletion N
Oryza rufipogon
(species)
Oryza sativa
rice - (species) D
Rc
Oryza sativa
rice - (species)
Published - Accepted by Curator
Rc
Coloration (seed)
Coding,
SNP
N
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Sweeney MT; Thomson MJ; Cho YG ; et al. (2007)
Global dissemination of a single mutation conferring white pericarp in rice.
2 Additional References
GP00000960
Rc
A7J5U6
Morphology
substitution; C->A in exon 6; introduces a premature stop codon (Cys>*) that truncates the protein before the bHLH domain N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Rc
Oryza sativa
rice - (species)
Published - Accepted by Curator
Rds2
Oxidative stress resistance
Coding,
SNP
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Diezmann S; Dietrich FS (2011)
Oxidative stress survival in a clinical Saccharomyces cerevisiae isolate is influenced by a major qu[...]
GP00000964
RDS2
P19541
Physiology
H251D
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
Rds2
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
REC114
Recombination rate
Unknown,
Unknown
Bos taurus
cattle - (species)
Domesticated
Association Mapping
Ma L; O'Connell JR; VanRaden PM ; et al. (2015)
Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.
GP00001661
REC114
Q7Z4M0
Physiology
On chromosome 10. Associated SNP located dowstream of the gene
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
REC114
Bos taurus
cattle - (species)
Published - Accepted by Curator
REC8
Recombination rate (male)
Cis-regulatory,
SNP
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Sandor C; Li W; Coppieters W ; et al. (2012)
Genetic variants in REC8, RNF212, and PRDM9 influence male recombination in cattle.
GP00001638
REC8
E1BL69
Physiology
A>G in intron 12 with reduction in Genome-wide recombination rate
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
REC8
Bos taurus
cattle - (species)
Published - Accepted by Curator
Reduced height-1 (Rht1)
Plant size (dwarfism)
Coding,
SNP
N
Helianthus annuus
common sunflower - (species) D
Domesticated
Linkage Mapping
Ramos ML; Altieri E; Bulos M ; et al. (2013)
Phenotypic characterization, genetic mapping and candidate gene analysis of a source conferring redu[...]
GP00001728
D8
Q9ST48
Morphology
T-to-C transition corresponding to nucleotide positions 143 - the SNP at position 143 converts a leucine residue in a proline within the conserved DELLA motif—This amino acid position corresponds to amino acid position 57 in the full-length amino acid sequence encoded by the L. sativa DELLA1 nucleotide sequence of GenBank Accession No. BAG71200.1 N
Helianthus annuus
common sunflower - (species)
Helianthus annuus
common sunflower - (species) D
Reduced height-1 (Rht1)
Helianthus annuus
common sunflower - (species)
Published - Accepted by Curator
Reduced height-B1 (RhtB1)
Plant size (dwarfism)
Coding,
SNP
N
Triticum aestivum
bread wheat - (species)
Domesticated
Linkage Mapping
Peng J; Richards DE; Hartley NM ; et al. (1999)
'Green revolution' genes encode mutant gibberellin response modulators.
GP00000965
D8
Q9ST48
Morphology
Q64*; TGA>CGA N
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species)
Reduced height-B1 (RhtB1)
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
Reduced height-D1 (RhtD1)
Plant size (dwarfism)
Coding,
SNP
N
Triticum aestivum
bread wheat - (species)
Domesticated
Linkage Mapping
Peng J; Richards DE; Hartley NM ; et al. (1999)
'Green revolution' genes encode mutant gibberellin response modulators.
GP00000966
D8
Q9ST48
Morphology
E61*; GGA>TGA N
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species)
Reduced height-D1 (RhtD1)
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
Resistance related Kinase 1 (RKS1)
Pathogen resistance (plant bacteria)
Coding,
SNP
Arabidopsis thaliana
thale cress - (species)
Domesticated
Linkage Mapping
Huard-Chauveau C; Perchepied L; Debieu M ; et al. (2013)
An atypical kinase under balancing selection confers broad-spectrum disease resistance in Arabidopsi[...]
GP00001599
F15B8.100
Q9SVY5
Physiology
a single-SNP difference in the coding region resulting in an amino acid change in the activation segment relative to the catalytic kinase loop. Other polymorphisms were found in the 5' and 3' regulatory regions. RKS1-L expression is 235.1 fold higher
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
Resistance related Kinase 1 (RKS1)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
retr02/eIF(iso)4E
Pathogen resistance (plant virus)
Coding,
SNP
Brassica rapa
field mustard - (species) D
Domesticated
Linkage Mapping
Qian W; Zhang S; Zhang S ; et al. (2013)
Mapping and candidate-gene screening of the novel Turnip mosaic virus resistance gene retr02 in Chin[...]
GP00000983
EIF(ISO)4E
O04663
Physiology
G152R
Brassica rapa
field mustard - (species)
Brassica rapa
field mustard - (species) D
retr02/eIF(iso)4E
Brassica rapa
field mustard - (species)
Published - Accepted by Curator
RGC2/Dm3
Pathogen resistance
Coding,
Unknown
Lactuca serriola
(species)
Domesticated
Linkage Mapping
Kuang H; Ochoa OE; Nevo E ; et al. (2006)
The disease resistance gene Dm3 is infrequent in natural populations of Lactuca serriola due to dele[...]
GP00000984
RGC2
Q6Y136
Physiology
Various haplotypes detected using PCR - absence of amplification could be due to deletion or to gene conversion
Lactuca serriola
(species)
Lactuca serriola
(species)
RGC2/Dm3
Lactuca serriola
(species)
Published - Accepted by Curator
Rgh4
Pathogen resistance (cyst nematode; parasite)
2 Mutations:
Coding
SNP
Glycine max
soybean - (species)
Domesticated
Linkage Mapping
Liu S; Kandoth PK; Warren SD ; et al. (2012)
A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens.
GP00001049
SHMT
K4FZF8
Physiology
2 mutations
Glycine max
soybean - (species)
Glycine max
soybean - (species)
Rgh4
Glycine max
soybean - (species)
Published - Accepted by Curator
ripening inhibitor (rin) = LeMADS-RIN and LeMADS-MC
Fruit ripening
Gene Loss,
Deletion
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Vrebalov J; Ruezinsky D; Padmanabhan V ; et al. (2002)
A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus.
1 Additional References
GP00000990
MADS-RIN
Q8S4L4
Physiology
2.6kb deletion of the region located between gene LeMADS-RIN and gene LeMADS-MC; resulting in a chimeric mRNA that contains both LeMADS-RIN and LeMADS-MC coding regions.
Solanum lycopersicum
tomato - (species)
Solanum lycopersicum
tomato - (species) D
ripening inhibitor (rin) = LeMADS-RIN and LeMADS-MC
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
RME1
Sporulation efficiency
Cis-regulatory,
Deletion
Saccharomyces cerevisiae
baker's yeast - (species) D
Domesticated
Linkage Mapping
Deutschbauer AM; Davis RW (2005)
Quantitative trait loci mapped to single-nucleotide resolution in yeast.
GP00000994
RME1
P32338
Physiology
single nucleotide deletion in promoter region
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species) D
RME1
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
RNF11
Body size (dwarfism)
Cis-regulatory,
Deletion
Bos taurus
cattle - (species) D
Domesticated
Association Mapping
Sartelet A; Druet T; Michaux C ; et al. (2012)
A splice site variant in the bovine RNF11 gene compromises growth and regulation of the inflammatory[...]
GP00002275
RNF11
Q9Y3C5
Morphology
g.95601696A>G c.124-2A>G affecting splicing site
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
RNF11
Bos taurus
cattle - (species)
Published - Accepted by Curator
RNF212
Recombination rate (male)
Coding,
SNP
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Sandor C; Li W; Coppieters W ; et al. (2012)
Genetic variants in REC8, RNF212, and PRDM9 influence male recombination in cattle.
GP00001639
RNF212
Q495C1
Physiology
T>C p.P259S in exon 12 with reduction in Genome-wide recombination rate
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
RNF212
Bos taurus
cattle - (species)
Published - Accepted by Curator
RORB
gait (saltatorial locomotion)
Coding,
SNP
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Association Mapping
Carneiro M; Vieillard J; Andrade P ; et al. (2021)
A loss-of-function mutation in RORB disrupts saltatorial locomotion in rabbits.
GP00002343
RORB
F1PET8
Behavior
a change from GT to AT in the 5’ donor site of intron 9 (chr1: 61,103,503bp). The mutation disrupts the normal splicing of RORB.
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
RORB
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
Rp1-D
Pathogen resistance
Gene Amplification,
Complex Change
Zea mays
(species)
Domesticated
Candidate Gene
Collins N; Drake J; Ayliffe M ; et al. (1999)
Molecular characterization of the maize Rp1-D rust resistance haplotype and its mutants.
2 Additional References
GP00000998
Rp1-D
Q9SWU0
Physiology
Unequal crossing over between paralogues resulting in chimeric gene
Zea mays
(species)
Zea mays
(species)
Rp1-D
Zea mays
(species)
Published - Accepted by Curator
Rp3 cluster
Pathogen resistance
Unknown,
Unknown
Zea mays
(species)
Domesticated
Linkage Mapping
Webb CA; Richter TE; Collins NC ; et al. (2002)
Genetic and molecular characterization of the maize rp3 rust resistance locus.
GP00000999
rp3-1
Q6PW75
Physiology
unknown
Zea mays
(species)
Zea mays
(species)
Rp3 cluster
Zea mays
(species)
Published - Accepted by Curator
RTA1
Xenobiotic resistance (citrinin)
Cis-regulatory,
Unknown
Saccharomyces paradoxus
(species) D
Domesticated
Association Mapping
Naranjo S; Smith JD; Artieri CG ; et al. (2015)
Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation.
GP00001312
RTA1
P53047
Physiology
unknown
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces paradoxus
(species) D
RTA1
Saccharomyces paradoxus
(species)
Published - Accepted by Curator
Ruby
Coloration (fruit; cold-dependent)
Cis-regulatory,
Insertion
Citrus sinensis
sweet orange - (species) D
Domesticated
Candidate Gene
Butelli E; Licciardello C; Zhang Y ; et al. (2012)
Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood orange[...]
GP00001017
Ruby
H6U1F1
Morphology
TE (Tcs2) insertion triggering cold-dependent expression
Citrus
(genus)
Citrus sinensis
sweet orange - (species) D
Ruby
Citrus sinensis
sweet orange - (species)
Published - Accepted by Curator
Ruby
Coloration (fruit; cold-dependent)
Cis-regulatory,
Insertion
Citrus sinensis
sweet orange - (species) D
Domesticated
Candidate Gene
Butelli E; Licciardello C; Zhang Y ; et al. (2012)
Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood orange[...]
GP00001018
Ruby
H6U1F1
Morphology
TE (Tcs1) insertion triggering cold-dependent expression
Citrus
(genus)
Citrus sinensis
sweet orange - (species) D
Ruby
Citrus sinensis
sweet orange - (species)
Published - Accepted by Curator
Ruby
Coloration (fruit; cold-dependent)
Cis-regulatory,
Deletion
Citrus sinensis
sweet orange - (species) D
Domesticated
Candidate Gene
Butelli E; Licciardello C; Zhang Y ; et al. (2012)
Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood orange[...]
GP00002106
Ruby
H6U1F1
Morphology
Recombination between the LTRs of the TE (Tcs1) insertion which led to just one LTR. The single LTR still confers responsiveness to cold temperatures. This recombination event results in enhanced expression of Ruby in Maro (I).
Citrus
(genus)
Citrus sinensis
sweet orange - (species) D
Ruby
Citrus sinensis
sweet orange - (species)
Published - Accepted by Curator
RXFP2
Horns absence
Somatic sex change
Gene Amplification,
Insertion
Ovis aries
sheep - (species)
Domesticated
Linkage Mapping
Johnston SE; Gratten J; Berenos C ; et al. (2013)
Life history trade-offs at a single locus maintain sexually selected genetic variation.
1 Additional References
GP00001019
RXFP2
Q8WXD0
Morphology
Physiology
1833-bp genomic insertion located in the 3'-UTR region of RXFP2
Ovis aries
sheep - (species)
Ovis aries
sheep - (species)
RXFP2
Ovis aries
sheep - (species)
Published - Accepted by Curator
RYR1
Meat content
Coding,
SNP
Sus scrofa
pig - (species) D
Domesticated
Linkage Mapping
Fujii J; Otsu K; Zorzato F ; et al. (1991)
Identification of a mutation in porcine ryanodine receptor associated with malignant hyperthermia.
GP00002338
Ryr1
E9PZQ0
Physiology
p.R615C
Sus scrofa
pig - (species)
Sus scrofa
pig - (species) D
RYR1
Sus scrofa
pig - (species)
Published - Accepted by Curator
S5
Hybrid incompatibility (F1 female sterility)
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Chen J; Ding J; Ouyang Y ; et al. (2008)
A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indi[...]
GP00001020
GRXS5
Q5QLR2
Physiology
2 non-synonymous changes Leu273Phe and Val471Ala segregate perfectly between japonica (Leu-Val) and japonica (Phe-Ala) - the effect of each amino acid chaeg has not been tested
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
S5
Oryza sativa
rice - (species)
Published - Accepted by Curator
S5 (ORF3-ORF4-ORF5 gene complex)
Hybrid incompatibility (sterility)
Coding,
Complex Change
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Yang J; Zhao X; Cheng K ; et al. (2012)
A killer-protector system regulates both hybrid sterility and segregation distortion in rice.
GP00001021
GRXS5
Q5QLR2
Physiology
System of alleles at three linked genes resulting in killer-protector system (hybrid incompabilitites)
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
S5 (ORF3-ORF4-ORF5 gene complex)
Oryza sativa
rice - (species)
Published - Accepted by Curator
sage
Silk yield
Cis-regulatory,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Association Mapping
Xia Q; Guo Y; Zhang Z ; et al. (2009)
Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx).
GP00002410
sage
Q9VHG3
Physiology
Increased expression in high yield strains. The sage gene encodes a transcription factor that activates glue genes in salivary glands of Drosophila melanogaster.
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
sage
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
SaM + SaF
Hybrid incompatibility (F1 male sterility)
Unknown,
Unknown
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Long Y; Zhao L; Niu B ; et al. (2008)
Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent ge[...]
1 Additional References
GP00001022
SaF+
B6RRX2
Physiology
Intron structure + aa changes on two adjacent coding genes
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
SaM + SaF
Oryza sativa
rice - (species)
Published - Accepted by Curator
SCARB1
Coloration (silk; carotenoids)
Cis-regulatory,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Sakudoh T; Iizuka T; Narukawa J ; et al. (2010)
A CD36-related transmembrane protein is coordinated with an intracellular lipid-binding protein in s[...]
GP00001905
Cameo2
D2KXB3
Morphology
difference in expression levels - three non synonymous mutations are also observed in the coding region - the gene is also named Cameo2
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
SCARB1
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
SCRB15
Coloration (silk; carotenoids)
Coding,
Insertion
N
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Sakudoh T; Kuwazaki S; Iizuka T ; et al. (2013)
CD36 homolog divergence is responsible for the selectivity of carotenoid species migration to the si[...]
GP00001904
SCRB15
K7ZRZ1
Morphology
In the F mutant SCRB15 mRNA structure was severely disrupted due to a 1.4 kb genomic insertion in a coding exon N
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
SCRB15
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (height)
2 Mutations:
Coding
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Asano K; Yamasaki M; Takuno S ; et al. (2011)
Artificial selection for a green revolution gene during japonica rice domestication.
GP00001027
GA20OX2
Q0JH50
Morphology
2 mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (dwarfism)
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Sasaki A; Ashikari M; Ueguchi-Tanaka M ; et al. (2002)
Green revolution: a mutant gibberellin-synthesis gene in rice.
3 Additional References
GP00001028
GA20OX2
Q0JH50
Morphology
383bp deletion introducing premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (dwarfism)
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Sasaki A; Ashikari M; Ueguchi-Tanaka M ; et al. (2002)
Green revolution: a mutant gibberellin-synthesis gene in rice.
GP00001029
GA20OX2
Q0JH50
Morphology
G94V
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (dwarfism)
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Sasaki A; Ashikari M; Ueguchi-Tanaka M ; et al. (2002)
Green revolution: a mutant gibberellin-synthesis gene in rice.
GP00001030
GA20OX2
Q0JH50
Morphology
D349H
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Sd1 (=GA20ox-2)
Plant size (dwarfism)
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Candidate Gene
Sasaki A; Ashikari M; Ueguchi-Tanaka M ; et al. (2002)
Green revolution: a mutant gibberellin-synthesis gene in rice.
GP00001031
GA20OX2
Q0JH50
Morphology
L266F
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Sd1 (=GA20ox-2)
Oryza sativa
rice - (species)
Published - Accepted by Curator
se5
Flowering time
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Izawa T; Oikawa T; Tokutomi S ; et al. (2000)
Phytochromes confer the photoperiodic control of flowering in rice (a short-day plant).
GP00001034
HO1
Q69XJ4
Physiology
1bp deletion in exon 1; causes a frameshift and a premature stop codon N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
se5
Oryza sativa
rice - (species)
Published - Accepted by Curator
SELF PRUNING 5G (SP5G)
Flowering time
Cis-regulatory,
Unknown
Solanum lycopersicum
tomato - (species)
Domesticated
Linkage Mapping
Soyk S; Müller NA; Park SJ ; et al. (2017)
Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato.
GP00001564
SP5G
Q84XK9
Physiology
several candidate SNPs and structural variants
Solanum pimpinellifolium
(species)
Solanum lycopersicum
tomato - (species)
SELF PRUNING 5G (SP5G)
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
self-pruning (sp)
Vegetative/Reproductive state switch
Coding,
SNP
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Pnueli L; Carmel-Goren L; Hareven D ; et al. (1998)
The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristem[...]
GP00001035
SP
O82088
Morphology
P76L due to CCT->CTT
Solanum lycopersicum
tomato - (species)
Solanum lycopersicum
tomato - (species) D
self-pruning (sp)
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
SGK3
Hair (hypotrichosis)
Coding,
Deletion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Parker HG; Harris A; Dreger DL ; et al. (2017)
The bald and the beautiful: hairlessness in domestic dog breeds.
GP00002262
Sgk3
Q9ERE3
Morphology
Val96GlyfsTer50 deletion that removes four bases (TTAG) within exon 4 ; creating a new protein sequence for 50 amino acids and a premature stop at amino acid 157 N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
SGK3
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
SGK3
Hair (hypotrichosis)
Coding,
Insertion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Association Mapping
Hytönen MK; Lohi H (2019)
A frameshift insertion in SGK3 leads to recessive hairlessness in Scottish Deerhounds: a candidate g[...]
1 Additional References
GP00002263
Sgk3
Q9ERE3
Morphology
c.137_138insT p.Glu47GlyfsTer3 N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
SGK3
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
SGLT1
Starch processing
Coding,
Unknown
Canis lupus familiaris
dog - (subspecies)
Domesticated
Association Mapping
Axelsson E; Ratnakumar A; Arendt ML ; et al. (2013)
The genomic signature of dog domestication reveals adaptation to a starch-rich diet.
GP00001037
Slc5a1
Q9QXI6
Physiology
unknown
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies)
SGLT1
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
Shattering1 - OsSh1
Seed shattering
Gene Loss,
Deletion
N
Oryza glaberrima
African rice - (species) D
Domesticated
Association Mapping
Wang M; Yu Y; Haberer G ; et al. (2014)
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication.
GP00001038
YAB2
Q10FZ7
Physiology
45kb deletion resulting in complete removal of OsSh1 in O. glaberrima; resulting in seed abscission phenotype N
Oryza barthii
(species)
Oryza glaberrima
African rice - (species) D
Shattering1 - OsSh1
Oryza glaberrima
African rice - (species)
Published - Accepted by Curator
Shattering1 - OsSh1
Seed shattering
Unknown,
Insertion
Oryza sativa
rice - (species) D
Domesticated
Association Mapping
Lin Z; Li X; Shannon LM ; et al. (2012)
Parallel domestication of the Shattering1 genes in cereals.
2 Additional References
GP00001039
YAB2
Q10FZ7
Physiology
>4kb insertion in intron (unclear)
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Shattering1 - OsSh1
Oryza sativa
rice - (species)
Published - Accepted by Curator
Shattering1 - Sh1
Seed shattering
Coding,
Deletion
N
Sorghum bicolor
sorghum - (species) D
Domesticated
Linkage Mapping
Lin Z; Li X; Shannon LM ; et al. (2012)
Parallel domestication of the Shattering1 genes in cereals.
GP00001040
YAB2
Q10FZ7
Physiology
2.2kb deletion at the location of exons 2 and 3 N
Sorghum virgatum
(species)
Sorghum bicolor
sorghum - (species) D
Shattering1 - Sh1
Sorghum bicolor
sorghum - (species)
Published - Accepted by Curator
Shattering1 - Sh1
Seed shattering
Coding,
Complex Change
Sorghum bicolor
sorghum - (species)
Domesticated
Linkage Mapping
Lin Z; Li X; Shannon LM ; et al. (2012)
Parallel domestication of the Shattering1 genes in cereals.
GP00001041
YAB2
Q10FZ7
Physiology
two promoter variants at positions -1194 and -1185
Sorghum virgatum
(species)
Sorghum bicolor
sorghum - (species)
Shattering1 - Sh1
Sorghum bicolor
sorghum - (species)
Published - Accepted by Curator
Shattering1 - Sh1
Seed shattering
Coding,
SNP
Sorghum bicolor
sorghum - (species)
Domesticated
Linkage Mapping
Lin Z; Li X; Shannon LM ; et al. (2012)
Parallel domestication of the Shattering1 genes in cereals.
GP00001042
YAB2
Q10FZ7
Physiology
GT-to-GG splice-site variant
Sorghum virgatum
(species)
Sorghum bicolor
sorghum - (species)
Shattering1 - Sh1
Sorghum bicolor
sorghum - (species)
Published - Accepted by Curator
Shattering1 - ZmSh1-1
Seed shattering
Coding,
Complex Change
Zea mays
(species)
Domesticated
Association Mapping
Lin Z; Li X; Shannon LM ; et al. (2012)
Parallel domestication of the Shattering1 genes in cereals.
GP00001043
YAB2
Q10FZ7
Physiology
complex structural variations
Zea mays
(species)
Zea mays
(species)
Shattering1 - ZmSh1-1
Zea mays
(species)
Published - Accepted by Curator
Shattering1 - ZmSh1-5.1 + ZmSh1-5.2
Seed shattering
Coding,
Unknown
Zea mays
(species)
Domesticated
Association Mapping
Lin Z; Li X; Shannon LM ; et al. (2012)
Parallel domestication of the Shattering1 genes in cereals.
GP00001044
YAB2
Q10FZ7
Physiology
various structural variations
Zea mays
(species)
Zea mays
(species)
Shattering1 - ZmSh1-5.1 + ZmSh1-5.2
Zea mays
(species)
Published - Accepted by Curator
shattering4 - sh4
Seed shattering
Cis-regulatory,
Unknown
Oryza glaberrima
African rice - (species) D
Domesticated
Association Mapping
Wang M; Yu Y; Haberer G ; et al. (2014)
The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication.
GP00001045
sh4
Q1PIH9
Physiology
several candidate mutations: ten SNPs and five small insertion/deletions leading to reduced expression
Oryza barthii
(species)
Oryza glaberrima
African rice - (species) D
shattering4 - sh4
Oryza glaberrima
African rice - (species)
Published - Accepted by Curator
shattering4 - sh4
Seed shattering
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Li C; Zhou A; Sang T (2006)
Rice domestication by reducing shattering.
GP00001046
sh4
Q1PIH9
Physiology
Asn -> Lys
Oryza rufipogon
(species)
Oryza sativa
rice - (species)
shattering4 - sh4
Oryza sativa
rice - (species)
Published - Accepted by Curator
SHELL
Fruit shell thickness
Coding,
SNP
Elaeis guineensis
African oil palm - (species)
Domesticated
Linkage Mapping
Singh R; Low ET; Ooi LC ; et al. (2013)
The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK.
GP00001047
AGL11
Q38836
Morphology
1a.a substitution in DNA binding domain
Elaeis guineensis
African oil palm - (species)
Elaeis guineensis
African oil palm - (species)
SHELL
Elaeis guineensis
African oil palm - (species)
Published - Accepted by Curator
SHELL
Fruit shell thickness
Coding,
SNP
Elaeis guineensis
African oil palm - (species)
Domesticated
Candidate Gene
Singh R; Low ET; Ooi LC ; et al. (2013)
The oil palm SHELL gene controls oil yield and encodes a homologue of SEEDSTICK.
GP00001048
AGL11
Q38836
Morphology
1a.a substitution in DNA binding domain
Elaeis guineensis
African oil palm - (species)
Elaeis guineensis
African oil palm - (species)
SHELL
Elaeis guineensis
African oil palm - (species)
Published - Accepted by Curator
shrunken-2 (Sh2) = endosperm ADP-glucose pyrophosphorylase large subunit
Feather
Cis-regulatory,
Insertion
Zea mays
(species) D
Domesticated
Linkage Mapping
Preiss J; Danner S; Summers PS ; et al. (1990)
Molecular Characterization of the Brittle-2 Gene Effect on Maize Endosperm ADPglucose Pyrophosphoryl[...]
1 Additional References
GP00001050
SH2
P55241
Physiology
insertion of the transposable element Dissociation
Zea mays
(species)
Zea mays
(species) D
shrunken-2 (Sh2) = endosperm ADP-glucose pyrophosphorylase large subunit
Zea mays
(species)
Published - Accepted by Curator
SKC1 =OsHKT1
Salt tolerance
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Ren ZH; Gao JP; Li LG ; et al. (2005)
A rice quantitative trait locus for salt tolerance encodes a sodium transporter.
GP00001055
HKT8
A2WNZ9
Physiology
several candidate missense mutations
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
SKC1 =OsHKT1
Oryza sativa
rice - (species)
Published - Accepted by Curator
SLC24A
Coloration (eyes)
Coding,
Deletion
N
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Mack M; Kowalski E; Grahn R ; et al. (2017)
Two Variants in SLC24A5 Are Associated with "Tiger-Eye" Iris Pigmentation in Puerto Rican Paso Fino [...]
GP00002276
Slc24a5
Q8C261
Morphology
628 bp deletion encompassing all of exon 7 of SLC24A5 (c.875-340_1081+82del) N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC24A
Equus caballus
horse - (species)
Published - Accepted by Curator
SLC24A
Coloration (eyes)
Coding,
SNP
N
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Mack M; Kowalski E; Grahn R ; et al. (2017)
Two Variants in SLC24A5 Are Associated with "Tiger-Eye" Iris Pigmentation in Puerto Rican Paso Fino [...]
GP00002277
Slc24a5
Q8C261
Morphology
c.272A>T p.Phe91Tyr N
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC24A
Equus caballus
horse - (species)
Published - Accepted by Curator
slc2a11b
Coloration (eyes)
Coding,
SNP
N
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Maclary ET; Phillips B; Wauer R ; et al. (2021)
Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia).
2 Additional References
GP00002367
slc2a11b
F6P601
Morphology
"The premature stop codon in pearl-eyed pigeons falls in exon 3 of SLC2A11B, and is predicted to severely truncate the resulting protein from 504 to 57 amino acids."
"Based on genotypes at the two coding SNPs in the pearl eye haplotype, we found that gene expression in embryo head samples only shows changes associated with the pearl eye haplotype in SLC2A11B, and not in any other genes within 15 kb of the pearl eye haplotype, further supporting SLC2A11B as the primary candidate for the pearl eye phenotype (supplementary fig. S3A, Supplementary Material online). Embryo heads homozygous for the pearl allele show a significant reduction in SLC2A11B expression (P = 3.94 × 10−6, two-tailed t-test; supplementary fig. S3B, Supplementary Material online). Analysis of read distribution within the SLC2A11B gene shows a decrease in spliced reads specifically within the first three annotated exons, suggesting that alternative splicing or nonsense-mediated decay may be occurring (supplementary fig. S3D, Supplementary Material online)." N
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
slc2a11b
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
SLC36A1
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Linkage Mapping
Cook D; Brooks S; Bellone R ; et al. (2008)
Missense mutation in exon 2 of SLC36A1 responsible for champagne dilution in horses.
GP00002278
SLC36A1
Q7Z2H8
Morphology
c.188C>G p.T63R
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC36A1
Equus caballus
horse - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Linkage Mapping
Mariat D; Taourit S; Guérin G (2003 Jan-Feb)
A mutation in the MATP gene causes the cream coat colour in the horse.
GP00001057
SLC45A2
Q9UMX9
Morphology
c.457G>A p.(Asp153Asn)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC45A2=MATP
Equus caballus
horse - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (feathers)
Coding,
SNP
Coturnix japonica
Japanese quail - (species)
Domesticated
Linkage Mapping
Gunnarsson U; Hellström AR; Tixier-Boichard M ; et al. (2007)
Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.
GP00001058
SLC45A2
Q9UMX9
Morphology
G->T transversion at the splice acceptor site just preceding exon 4; causes in-frame skipping of exon 4
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species)
SLC45A2=MATP
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (feathers)
Coding,
Deletion
N
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Gunnarsson U; Hellström AR; Tixier-Boichard M ; et al. (2007)
Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.
GP00001059
SLC45A2
Q9UMX9
Morphology
1bp deletion at codon 36; resulting in frameshift and a premature stop codon in exon 1; the corresponding mRNA appears to be degraded by Nonsense-mediated mRNA decay. N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SLC45A2=MATP
Gallus gallus
chicken - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (eyes; fur)
Coding,
SNP
Mus musculus
house mouse - (species)
Domesticated
Linkage Mapping
Du J; Fisher DE (2002)
Identification of Aim-1 as the underwhite mouse mutant and its transcriptional regulation by MITF.
GP00001060
SLC45A2
Q9UMX9
Morphology
N153D
Mus musculus
house mouse - (species)
Mus musculus
house mouse - (species)
SLC45A2=MATP
Mus musculus
house mouse - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (feathers)
Coding,
SNP
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014)
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
GP00001062
SLC45A2
Q9UMX9
Morphology
His341Arg
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
SLC45A2=MATP
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat; albinism)
Coding,
SNP
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Rothammer S; Kunz E; Seichter D ; et al. (2017)
Detection of two non-synonymous SNPs in SLC45A2 on BTA20 as candidate causal mutations for oculocuta[...]
GP00002036
SLC45A2
Q9UMX9
Morphology
exact causing mutation(s) unknown - two possible amino acid changes
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
SLC45A2=MATP
Bos taurus
cattle - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (albinism)
Coding,
Insertion
Oryzias latipes
Japanese medaka - (species) D
Domesticated
Linkage Mapping
Fukamachi S; Shimada A; Shima A (2001)
Mutations in the gene encoding B, a novel transporter protein, reduce melanin content in medaka.
GP00002286
SLC45A2
Q9UMX9
Morphology
tandem insertion of 195 nt identical to the adjacent ORF sequence. This tandem repeat produces an insertion of 65 amino acids
Oryzias latipes
Japanese medaka - (species)
Oryzias latipes
Japanese medaka - (species) D
SLC45A2=MATP
Oryzias latipes
Japanese medaka - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (albinism)
Cis-regulatory,
Complex Change
Oryzias latipes
Japanese medaka - (species) D
Domesticated
Candidate Gene
Fukamachi S; Kinoshita M; Tsujimura T ; et al. (2008)
Rescue from oculocutaneous albinism type 4 using medaka slc45a2 cDNA driven by its own promoter.
GP00002287
SLC45A2
Q9UMX9
Morphology
Promoter complex change resulting in loss of expression : an inversion of 167 bp ; an insertion of 48 bp ; and a deletion of 172 bp
Oryzias latipes
Japanese medaka - (species)
Oryzias latipes
Japanese medaka - (species) D
SLC45A2=MATP
Oryzias latipes
Japanese medaka - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (feathers)
Coding,
SNP
N
Gallus gallus
chicken - (species) D
Domesticated
Association Mapping
Gunnarsson U; Hellström AR; Tixier-Boichard M ; et al. (2007)
Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.
GP00002294
SLC45A2
Q9UMX9
Morphology
c.1039C>A p.L347M N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SLC45A2=MATP
Gallus gallus
chicken - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (feathers)
Coding,
SNP
N
Gallus gallus
chicken - (species) D
Domesticated
Association Mapping
Gunnarsson U; Hellström AR; Tixier-Boichard M ; et al. (2007)
Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.
GP00002295
SLC45A2
Q9UMX9
Morphology
c.830A>G p.Y277C N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SLC45A2=MATP
Gallus gallus
chicken - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat; albinism)
Coding,
Deletion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Winkler PA; Gornik KR; Ramsey DT ; et al. (2014)
A partial gene deletion of SLC45A2 causes oculocutaneous albinism in Doberman pinscher dogs.
GP00002296
SLC45A2
Q9UMX9
Morphology
4081 base pair deletion resulting in loss of the terminus of exon seven of SLC45A2 N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
SLC45A2=MATP
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat; albinism)
Coding,
SNP
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Wijesena HR; Schmutz SM (2015 May-Jun)
A Missense Mutation in SLC45A2 Is Associated with Albinism in Several Small Long Haired Dog Breeds.
GP00002297
SLC45A2
Q9UMX9
Morphology
c.1478G>A p.G493D N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
SLC45A2=MATP
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat; albinism)
Coding,
Deletion
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Caduff M; Bauer A; Jagannathan V ; et al. (2017)
A single base deletion in the SLC45A2 gene in a Bullmastiff with oculocutaneous albinism.
GP00002298
SLC45A2
Q9UMX9
Morphology
c.1287delC p.Met430CysfsTer4 N
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
SLC45A2=MATP
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Sevane N; Sanz CR; Dunner S (2019)
Explicit evidence for a missense mutation in exon 4 of SLC45A2 gene causing the pearl coat dilution [...]
GP00002304
SLC45A2
Q9UMX9
Morphology
c.985G>A p.(Ala329Thr)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC45A2=MATP
Equus caballus
horse - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Holl HM; Pflug KM; Yates KM ; et al. (2019)
A candidate gene approach identifies variants in SLC45A2 that explain dilute phenotypes, pearl and s[...]
GP00002305
SLC45A2
Q9UMX9
Morphology
c.568G>A p.(Gly190Arg)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC45A2=MATP
Equus caballus
horse - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (coat)
Coding,
SNP
Equus caballus
horse - (species) D
Domesticated
Candidate Gene
Holl HM; Pflug KM; Yates KM ; et al. (2019)
A candidate gene approach identifies variants in SLC45A2 that explain dilute phenotypes, pearl and s[...]
GP00002306
SLC45A2
Q9UMX9
Morphology
c.305G>A p.(Arg102Gln)
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
SLC45A2=MATP
Equus caballus
horse - (species)
Published - Accepted by Curator
SLC45A2=MATP
Coloration (feathers)
Coding,
SNP
Coturnix japonica
Japanese quail - (species)
Domesticated
Linkage Mapping
Gunnarsson U; Hellström AR; Tixier-Boichard M ; et al. (2007)
Mutations in SLC45A2 cause plumage color variation in chicken and Japanese quail.
GP00002307
SLC45A2
Q9UMX9
Morphology
c.287C>A p.A72D
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species)
SLC45A2=MATP
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
SLCO1B3
Coloration (blue eggs)
Cis-regulatory,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Wang Z; Qu L; Yao J ; et al. (2013)
An EAV-HP insertion in 5' Flanking region of SLCO1B3 causes blue eggshell in the chicken.
GP00001064
SLCO1B3
Q9NPD5
Morphology
TE (EAV-HP) promoter insertion resulting in uterus expression
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SLCO1B3
Gallus gallus
chicken - (species)
Published - Accepted by Curator
SLCO1B3
Coloration (blue eggs)
Cis-regulatory,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Wang Z; Qu L; Yao J ; et al. (2013)
An EAV-HP insertion in 5' Flanking region of SLCO1B3 causes blue eggshell in the chicken.
GP00001065
SLCO1B3
Q9NPD5
Morphology
TE (EAV-HP) promoter insertion resulting in uterus expression
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SLCO1B3
Gallus gallus
chicken - (species)
Published - Accepted by Curator
SMAD family member 2 (SMAD2)
Body size (weight)
Cis-regulatory,
Deletion
Homo sapiens
human - (species) D
Domesticated
Association Mapping
Rimbault M; Beale HC; Schoenebeck JJ ; et al. (2013)
Derived variants at six genes explain nearly half of size reduction in dog breeds.
GP00001477
SMAD2
E2RP23
Morphology
9.9 kb deletion 24-kb dowstream from coding region
Canis lupus
gray wolf - (species)
Homo sapiens
human - (species) D
SMAD family member 2 (SMAD2)
Homo sapiens
human - (species)
Published - Accepted by Curator
SMC3
Recombination rate (female)
Unknown,
Unknown
Bos taurus
cattle - (species)
Domesticated
Association Mapping
Ma L; O'Connell JR; VanRaden PM ; et al. (2015)
Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.
GP00001666
SMC3
O97594
Physiology
On chromosome 26. Associated SNP located upstream
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
SMC3
Bos taurus
cattle - (species)
Published - Accepted by Curator
SOX10
Coloration (feathers)
Cis-regulatory,
Deletion
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014)
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
GP00001067
Sox10
Q04888
Morphology
melanocyte conserved enhancer deletion
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
SOX10
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
SOX10
Coloration (feathers)
Cis-regulatory,
Deletion
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014)
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
GP00001068
Sox10
Q04888
Morphology
melanocyte conserved enhancer deletion
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
SOX10
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
SOX10
Coloration (feathers)
Cis-regulatory,
Deletion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Gunnarsson U; Kerje S; Bed'hom B ; et al. (2011)
The Dark brown plumage color in chickens is caused by an 8.3-kb deletion upstream of SOX10.
1 Additional References
GP00001069
Sox10
Q04888
Morphology
8.3kb deletion upstream of the SOX10 transcription start site
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SOX10
Gallus gallus
chicken - (species)
Published - Accepted by Curator
SOX5
Bird head comb (reduced comb and wattles)
Cis-regulatory,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Wright D; Boije H; Meadows JR ; et al. (2009)
Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens.
GP00001070
Sox5
P35710
Morphology
Copy Number Variation in Intron 1 - about 30 copies of a 3 kb sequence - corresponding to about 85 kb of extra sequence
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
SOX5
Gallus gallus
chicken - (species)
Published - Accepted by Curator
srg-34
Diapause (resistance to dauer-inducing pheromone)
Gene Loss,
Deletion
N
Caenorhabditis briggsae
(species)
Domesticated
Linkage Mapping
McGrath PT; Xu Y; Ailion M ; et al. (2011)
Parallel evolution of domesticated Caenorhabditis species targets pheromone receptor genes.
GP00001074
srg-34
Q9XXQ5
Physiology
33kb deletion N
Caenorhabditis briggsae
(species)
Caenorhabditis briggsae
(species)
srg-34
Caenorhabditis briggsae
(species)
Published - Accepted by Curator
srg-36/37
Diapause (resistance to dauer-inducing pheromone)
Gene Loss,
Deletion
N
Caenorhabditis elegans
(species)
Domesticated
Linkage Mapping
McGrath PT; Xu Y; Ailion M ; et al. (2011)
Parallel evolution of domesticated Caenorhabditis species targets pheromone receptor genes.
GP00001075
srg-34
Q9XXQ5
Physiology
6795bp deletion N
Caenorhabditis elegans
(species)
Caenorhabditis elegans
(species)
srg-36/37
Caenorhabditis elegans
(species)
Published - Accepted by Curator
srg-36/37
Diapause (resistance to dauer-inducing pheromone)
Gene Loss,
Deletion
N
Caenorhabditis elegans
(species)
Domesticated
Linkage Mapping
McGrath PT; Xu Y; Ailion M ; et al. (2011)
Parallel evolution of domesticated Caenorhabditis species targets pheromone receptor genes.
GP00001076
srg-34
Q9XXQ5
Physiology
4906bp deletion N
Caenorhabditis elegans
(species)
Caenorhabditis elegans
(species)
srg-36/37
Caenorhabditis elegans
(species)
Published - Accepted by Curator
stanniocalcin 2 (STC2)
Body size (weight)
Cis-regulatory,
SNP
Homo sapiens
human - (species) D
Domesticated
Association Mapping
Rimbault M; Beale HC; Schoenebeck JJ ; et al. (2013)
Derived variants at six genes explain nearly half of size reduction in dog breeds.
GP00001478
STC2
O76061
Morphology
T>A 20-kb downstream from coding region
Canis lupus
gray wolf - (species)
Homo sapiens
human - (species) D
stanniocalcin 2 (STC2)
Homo sapiens
human - (species)
Published - Accepted by Curator
Starch branching enzyme (SBEI) = rugosus (R)
Starch structure
Seed aspect
Coding,
Insertion
N
Pisum sativum
pea - (species) D
Domesticated
Linkage Mapping
Bhattacharyya MK; Smith AM; Ellis TH ; et al. (1990)
The wrinkled-seed character of pea described by Mendel is caused by a transposon-like insertion in a[...]
GP00001078
SBEI
Q41058
Physiology
Morphology
800 bp TE insertion; probably disrupts the last 61 amino acids of the SBEI protein N
Pisum sativum
pea - (species)
Pisum sativum
pea - (species) D
Starch branching enzyme (SBEI) = rugosus (R)
Pisum sativum
pea - (species)
Published - Accepted by Curator
StCDF1
Latitudinal adaptation
Coding,
Insertion
N
Solanum tuberosum
potato - (species) D
Domesticated
Linkage Mapping
Kloosterman B; Abelenda JA; Gomez Mdel M ; et al. (2013)
Naturally occurring allele diversity allows potato cultivation in northern latitudes.
GP00001079
CDF1
Q8W1E3
Physiology
+7bp insertion resulting in frameshift and truncated protein N
Solanum tuberosum
potato - (species)
Solanum tuberosum
potato - (species) D
StCDF1
Solanum tuberosum
potato - (species)
Published - Accepted by Curator
StCDF1
Latitudinal adaptation
Coding,
Insertion
Solanum tuberosum
potato - (species) D
Domesticated
Linkage Mapping
Kloosterman B; Abelenda JA; Gomez Mdel M ; et al. (2013)
Naturally occurring allele diversity allows potato cultivation in northern latitudes.
GP00001080
CDF1
Q8W1E3
Physiology
865bp insertion leading to a fusion protein
Solanum tuberosum
potato - (species)
Solanum tuberosum
potato - (species) D
StCDF1
Solanum tuberosum
potato - (species)
Published - Accepted by Curator
Style2.1
Flower morphology (style length)
Autogamy
Cis-regulatory,
Unknown
Solanum lycopersicum
tomato - (species) D
Domesticated
Linkage Mapping
Chen KY; Cong B; Wing R ; et al. (2007)
Changes in regulation of a transcription factor lead to autogamy in cultivated tomatoes.
GP00001081
100301942
B6CG44
Morphology
Physiology
Not identified
Solanum pennellii
(species)
Solanum lycopersicum
tomato - (species) D
Style2.1
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
sugary 1 (su1) = isoamylase-type starch-debranching enzymes
Fruit sugar content
Coding,
SNP
Zea mays
(species)
Domesticated
Candidate Gene
Dinges JR; Colleoni C; Myers AM ; et al. (2001)
Molecular structure of three mutations at the maize sugary1 locus and their allele-specific phenotyp[...]
1 Additional References
GP00001082
sugary1
O22637
Physiology
F163L and/or W578R; W738R is more likely to be the mutation responsible as it affect a residue conserved in plants and bacteria
Zea mays
(species)
Zea mays
(species)
sugary 1 (su1) = isoamylase-type starch-debranching enzymes
Zea mays
(species)
Published - Accepted by Curator
SUN
Fruit shape
Gene Amplification,
Complex Change
Solanum lycopersicum
tomato - (species)
Domesticated
Linkage Mapping
Xiao H; Jiang N; Schaffner E ; et al. (2008)
A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit.
GP00001084
100147716
B1N669
Morphology
Gene duplication
Solanum pimpinellifolium
(species)
Solanum lycopersicum
tomato - (species)
SUN
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
SWS2
Xenobiotic resistance (alcohol, ethanol)
Cis-regulatory,
Unknown
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Swinnen S; Schaerlaekens K; Pais T ; et al. (2012)
Identification of novel causative genes determining the complex trait of high ethanol tolerance in y[...]
GP00001088
SWS2
P53937
Physiology
unknown
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
SWS2
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
SWS2
Sporulation efficiency
Cis-regulatory,
Unknown
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Ben-Ari G; Zenvirth D; Sherman A ; et al. (2006)
Four linked genes participate in controlling sporulation efficiency in budding yeast.
GP00001089
SWS2
P53937
Physiology
unknown
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
SWS2
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
syntaxin-17
Coloration (hair ; graying with age)
Cis-regulatory,
Insertion
Equus caballus
horse - (species) D
Domesticated
Association Mapping
Rosengren Pielberg G; Golovko A; Sundström E ; et al. (2008)
A cis-acting regulatory mutation causes premature hair graying and susceptibility to melanoma in the[...]
2 Additional References
GP00002272
STX17
P56962
Morphology
4.6-kb duplication in intron 6 of STX17 ; in transgenic zebrafish a construct containing two copies of the duplicated sequence acts as a strong enhancer in neural crest cells and has subsequent melanophore-specific activity whereas a single copy of the duplicated sequence acts as a weak enhancer - consistent with the phenotypic manifestation of the mutation in horses
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
syntaxin-17
Equus caballus
horse - (species)
Published - Accepted by Curator
T-box transcription factor (TBX3)
Coloration (coat)
Cis-regulatory,
Deletion
Equus caballus
horse - (species) D
Domesticated
Linkage Mapping
Imsland F; McGowan K; Rubin CJ ; et al. (2016)
Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage colo[...]
GP00001462
TBX3
O15119
Morphology
missing sequence of nearly contiguous 1609bp and 8 bp segments
Equus caballus
horse - (species)
Equus caballus
horse - (species) D
T-box transcription factor (TBX3)
Equus caballus
horse - (species)
Published - Accepted by Curator
TAO3
Sporulation efficiency
Cis-regulatory,
SNP
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Deutschbauer AM; Davis RW (2005)
Quantitative trait loci mapped to single-nucleotide resolution in yeast.
GP00001103
TAO3
P40468
Physiology
E1493Q
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
TAO3
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
TaPHS1
Seed dormancy
Coding,
SNP
N
Triticum aestivum
bread wheat - (species)
Domesticated
Linkage Mapping
Liu S; Sehgal SK; Li J ; et al. (2013)
Cloning and characterization of a critical regulator for preharvest sprouting in wheat.
GP00001104
PHS1
D2J2Y0
Physiology
GT-to-AT transition at the 5_ donor splice site (position +646) of intron 3 AND Premature Stop Codon (position +666) N
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species)
TaPHS1
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
Tbx5
Limb Identity (feathered feet)
Cis-regulatory,
Unknown
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Kronenberg Z; Infante CR ; et al. (2016)
Molecular shifts in limb identity underlie development of feathered feet in two domestic avian speci[...]
GP00001114
TBX5
Q9PWE8
Morphology
unknown
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
Tbx5
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
TBXT
Organ size (tail; short)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Zhi D; Da L; Liu M ; et al. (2018)
Whole Genome Sequencing of Hulunbuir Short-Tailed Sheep for Identifying Candidate Genes Related to t[...]
1 Additional References
GP00002289
Tbxt
P20293
Morphology
c.G334T p.G112W
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
TBXT
Ovis aries
sheep - (species)
Published - Accepted by Curator
TBXT
Organ size (tail; short)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Buckingham KJ; McMillin MJ; Brassil MM ; et al. (2013)
Multiple mutant T alleles cause haploinsufficiency of Brachyury and short tails in Manx cats.
GP00002290
Tbxt
P20293
Morphology
c.1169delC N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
TBXT
Felis catus
domestic cat - (species)
Published - Accepted by Curator
TBXT
Organ size (tail; short)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Buckingham KJ; McMillin MJ; Brassil MM ; et al. (2013)
Multiple mutant T alleles cause haploinsufficiency of Brachyury and short tails in Manx cats.
GP00002291
Tbxt
P20293
Morphology
c.1199delC N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
TBXT
Felis catus
domestic cat - (species)
Published - Accepted by Curator
TBXT
Organ size (tail; short)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Buckingham KJ; McMillin MJ; Brassil MM ; et al. (2013)
Multiple mutant T alleles cause haploinsufficiency of Brachyury and short tails in Manx cats.
GP00002292
Tbxt
P20293
Morphology
c.998delT N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
TBXT
Felis catus
domestic cat - (species)
Published - Accepted by Curator
TBXT
Organ size (tail; short)
Coding,
Indel
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Buckingham KJ; McMillin MJ; Brassil MM ; et al. (2013)
Multiple mutant T alleles cause haploinsufficiency of Brachyury and short tails in Manx cats.
GP00002293
Tbxt
P20293
Morphology
c.998_1014dup17delGCC N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
TBXT
Felis catus
domestic cat - (species)
Published - Accepted by Curator
TBXT
Organ size (tail; short)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Linkage Mapping
Haworth K; Putt W; Cattanach B ; et al. (2001)
Canine homolog of the T-box transcription factor T; failure of the protein to bind to its DNA target[...]
3 Additional References
GP00002340
Tbxt
P20293
Morphology
c.189C>G p.I63M
Canis lupus familiaris
dog - (subspecies)
Canis lupus familiaris
dog - (subspecies) D
TBXT
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
teosinte branched 1 (tb1)
Plant architecture
Inflorescence architecture
Cis-regulatory,
Insertion
Zea mays
(species) D
Domesticated
Linkage Mapping
Clark RM; Wagler TN; Quijada P ; et al. (2006)
A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and[...]
2 Additional References
GP00001116
TB1
Q93WI2
Morphology
Morphology
Hopscotch TE insertion
Zea mays
(species)
Zea mays
(species) D
teosinte branched 1 (tb1)
Zea mays
(species)
Published - Accepted by Curator
teosinte branched 1 (tb1) = IntC
Plant architecture
Inflorescence architecture
Coding,
Unknown
Hordeum vulgare
(species)
Domesticated
Association Mapping
Ramsay L; Comadran J; Druka A ; et al. (2011)
INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domes[...]
GP00001117
TB1
Q93WI2
Morphology
Morphology
Large haplotypes; unknown
Hordeum vulgare
(species)
Hordeum vulgare
(species)
teosinte branched 1 (tb1) = IntC
Hordeum vulgare
(species)
Published - Accepted by Curator
teosinte glume architecture (tga1)
Cupule retraction
Coding,
SNP
Zea mays
(species)
Domesticated
Linkage Mapping
Wang H; Nussbaum-Wagler T; Li B ; et al. (2005)
The origin of the naked grains of maize.
GP00001118
TGA1
Q39237
Morphology
K6N; the lysine residue being conserved in rice and wheat
Zea mays
(species)
Zea mays
(species)
teosinte glume architecture (tga1)
Zea mays
(species)
Published - Accepted by Curator
TFL1 / HvCEN
Growth determination habit
Coding,
SNP
Hordeum vulgare
(species)
Domesticated
Linkage Mapping
Comadran J; Kilian B; Russell J ; et al. (2012)
Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and [...]
GP00001119
TFL1
P93003
Physiology
P135A
Hordeum vulgare
(species)
Hordeum vulgare
(species)
TFL1 / HvCEN
Hordeum vulgare
(species)
Published - Accepted by Curator
TFL1/GmTFL1
Growth determination habit
Coding,
SNP
Glycine max
soybean - (species)
Domesticated
Linkage Mapping
Tian Z; Wang X; Lee R ; et al. (2010)
Artificial selection for determinate growth habit in soybean.
GP00001121
TFL1
P93003
Physiology
R62S
Glycine max
soybean - (species)
Glycine max
soybean - (species)
TFL1/GmTFL1
Glycine max
soybean - (species)
Published - Accepted by Curator
TFL1/GmTFL1
Growth determination habit
Coding,
SNP
Glycine max
soybean - (species)
Domesticated
Candidate Gene
Tian Z; Wang X; Lee R ; et al. (2010)
Artificial selection for determinate growth habit in soybean.
GP00001122
TFL1
P93003
Physiology
P113L
Glycine max
soybean - (species)
Glycine max
soybean - (species)
TFL1/GmTFL1
Glycine max
soybean - (species)
Published - Accepted by Curator
TFL1/GmTFL1
Growth determination habit
Coding,
SNP
Glycine max
soybean - (species)
Domesticated
Candidate Gene
Tian Z; Wang X; Lee R ; et al. (2010)
Artificial selection for determinate growth habit in soybean.
GP00001123
TFL1
P93003
Physiology
R130K
Glycine max
soybean - (species)
Glycine max
soybean - (species)
TFL1/GmTFL1
Glycine max
soybean - (species)
Published - Accepted by Curator
TFL1/GmTFL1
Growth determination habit
Coding,
SNP
Glycine max
soybean - (species)
Domesticated
Candidate Gene
Tian Z; Wang X; Lee R ; et al. (2010)
Artificial selection for determinate growth habit in soybean.
GP00001124
TFL1
P93003
Physiology
R166W
Glycine max
soybean - (species)
Glycine max
soybean - (species)
TFL1/GmTFL1
Glycine max
soybean - (species)
Published - Accepted by Curator
THOUSAND-GRAIN WEIGHT 6 (TGW6)
Grain yield
Coding,
Deletion
N
Oryza sativa
rice - (species) D
Domesticated
Linkage Mapping
Ishimaru K; Hirotsu N; Madoka Y ; et al. (2013)
Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yie[...]
GP00001126
TGW6
Q69U01
Morphology
-1bp at +313 resulting in truncated protein N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
THOUSAND-GRAIN WEIGHT 6 (TGW6)
Oryza sativa
rice - (species)
Published - Accepted by Curator
Thyroid stimulating hormone receptor
Metabolism
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Association Mapping
Rubin CJ; Zody MC; Eriksson J ; et al. (2010)
Whole-genome resequencing reveals loci under selection during chicken domestication.
1 Additional References
GP00001127
TSHR
P16473
Physiology
Gly558Arg
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
Thyroid stimulating hormone receptor
Gallus gallus
chicken - (species)
Published - Accepted by Curator
TICAM1
Pathogen resistance (Trypanosoma)
Coding,
Unknown
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Noyes H; Brass A; Obara I ; et al. (2011)
Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypa[...]
GP00001128
TICAM1
Q8IUC6
Physiology
unknown
Bos
oxen, cattle - (genus)
Bos taurus
cattle - (species)
TICAM1
Bos taurus
cattle - (species)
Published - Accepted by Curator
TMEM263
Body size (dwarfism)
Coding,
SNP
N
Gallus gallus
chicken - (species) D
Domesticated
Linkage Mapping
Wu Z; Derks MFL; Dibbits B ; et al. (2018)
A Novel Loss-of-Function Variant in Transmembrane Protein 263 (TMEM263) of Autosomal Dwarfism in Chi[...]
GP00002161
Physiology
g.53688583C>T c.433G>A p.Trp59∗ N
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
TMEM263
Gallus gallus
chicken - (species)
Published - Accepted by Curator
Tret1-like
Diapause
Cis-regulatory,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Association Mapping
Tong X; Han MJ; Lu K ; et al. (2022)
High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecologic[...]
GP00002402
Tret1-1
A1Z8N1
Physiology
The expression level of BmTret1-like in homozygotes (pnd/pnd) is significantly lower (p < 0.01, t test) than that in heterozygotes (pnd/+). CRISPR BmTret1-like knockout lines generate non-diapause eggs. A 747 bp deletion is present in the 3′-untranslated region (3′-UTR) of BmTret1-like in pnd homozygotes
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Tret1-like
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
TRK1
Salt tolerance (ammonium)
Coding,
SNP
Saccharomyces cerevisiae
baker's yeast - (species)
Domesticated
Linkage Mapping
Reisser C; Dick C; Kruglyak L ; et al. (2013)
Genetic Basis of Ammonium Toxicity Resistance in a Sake Strain of Yeast: A Mendelian Case.
GP00001139
NTRK1
P04629
Physiology
Candidate a.a substitutions in K12 : C1143S; H551P; E1190G; Q1227K
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species)
TRK1
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
TRPV4
Ear size (drop)
Coding,
SNP
Felis catus
domestic cat - (species) D
Domesticated
Association Mapping
Gandolfi B; Alamri S; Darby WG ; et al. (2016)
A dominant TRPV4 variant underlies osteochondrodysplasia in Scottish fold cats.
1 Additional References
GP00002279
TRPV4
Q9HBA0
Morphology
c.1024G>T p.V342F
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
TRPV4
Felis catus
domestic cat - (species)
Published - Accepted by Curator
TT8
Coloration (seed)
Coding,
Insertion
N
Brassica rapa
field mustard - (species) D
Domesticated
Linkage Mapping
Li X; Chen L; Hong M ; et al. (2012)
A large insertion in bHLH transcription factor BrTT8 resulting in yellow seed coat in Brassica rapa.
GP00002077
TT8
Q9FT81
Morphology
insertion of a Helitron transposon of 4320 bp in intron 2 starting with 5' TC and ending with 3'CTAG containing a 17 bp palindromic region forming a hairpin - prevents transcription N
Brassica rapa
field mustard - (species)
Brassica rapa
field mustard - (species) D
TT8
Brassica rapa
field mustard - (species)
Published - Accepted by Curator
Twist1
Horn shape (scurs)
Coding,
Insertion
N
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Capitan A; Grohs C; Weiss B ; et al. (2011)
A newly described bovine type 2 scurs syndrome segregates with a frame-shift mutation in TWIST1.
GP00002034
Twist1
P26687
Morphology; Physiology
small duplication (c.148_157dup (p.A56RfsX87)) that causes a frameshift and inactivates the gene. N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Twist1
Bos taurus
cattle - (species)
Published - Accepted by Curator
Twist2
Coloration (coat; white belt)
Cis-regulatory,
Insertion
Bos taurus
cattle - (species) D
Domesticated
Linkage Mapping
Awasthi Mishra N; Drögemüller C; Jagannathan V ; et al. (2017)
A structural variant in the 5'-flanking region of the TWIST2 gene affects melanocyte development in [...]
2 Additional References
GP00002035
Twist2
Q9D030
Morphology
quadruplication (CNV) of a 6 kb non-coding sequence located approximately 16 kb upstream of the TWIST2 gene
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
Twist2
Bos taurus
cattle - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Felis catus
domestic cat - (species) D
Domesticated
Linkage Mapping
Lyons LA; Imes DL; Rah HC ; et al. (2005)
Tyrosinase mutations associated with Siamese and Burmese patterns in the domestic cat (Felis catus).
1 Additional References
GP00001142
Tyr
P11344
Morphology
c.679G>T p.G227W
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase (TYR)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Felis catus
domestic cat - (species) D
Domesticated
Linkage Mapping
Lyons LA; Imes DL; Rah HC ; et al. (2005)
Tyrosinase mutations associated with Siamese and Burmese patterns in the domestic cat (Felis catus).
1 Additional References
GP00001143
Tyr
P11344
Morphology
c. 940G>A p.G302R
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase (TYR)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (feathers)
Coding,
Deletion
Gallus gallus
chicken - (species) D
Domesticated
Candidate Gene
Tobita-Teramoto T; Jang GY; Kino K ; et al. (2000)
Autosomal albino chicken mutation (ca/ca) deletes hexanucleotide (-deltaGACTGG817) at a copper-bindi[...]
GP00002308
Tyr
P11344
Morphology
c.817_822del6 p.237-238delDW
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
tyrosinase (TYR)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (feathers)
Coding,
Insertion
Gallus gallus
chicken - (species) D
Domesticated
Candidate Gene
Chang CM; Coville JL; Coquerelle G ; et al. (2006)
Complete association between a retroviral insertion in the tyrosinase gene and the recessive white m[...]
GP00002309
Tyr
P11344
Morphology
insertion of a complete avian retroviral sequence in intron 4 causes aberrant transcripts lacking exon 5
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species) D
tyrosinase (TYR)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
Deletion
Mustela putorius furo
domestic ferret - (subspecies) D
Domesticated
Linkage Mapping
Blaszczyk WM; Distler C; Dekomien G ; et al. (2007)
Identification of a tyrosinase (TYR) exon 4 deletion in albino ferrets (Mustela putorius furo).
GP00002310
Tyr
P11344
Morphology
Deletion of exon 4 as detected by Southern Blot
Mustela putorius furo
domestic ferret - (subspecies)
Mustela putorius furo
domestic ferret - (subspecies) D
tyrosinase (TYR)
Mustela putorius furo
domestic ferret - (subspecies)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
Indel
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Yu Y; Grahn RA; Lyons LA (2019)
Mocha tyrosinase variant: a new flavour of cat coat coloration.
GP00002311
Tyr
P11344
Morphology
c.820_936delinsAATCTC p.I274_L312delinsNL
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase (TYR)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
Deletion
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Imes DL; Geary LA; Grahn RA ; et al. (2006)
Albinism in the domestic cat (Felis catus) is associated with a tyrosinase (TYR) mutation.
GP00002312
Tyr
P11344
Morphology
a cytosine deletion in TYR at position 975 in exon 2 N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase (TYR)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
N
Felis catus
domestic cat - (species) D
Domesticated
Candidate Gene
Abitbol M; Bossé P; Grimard B ; et al. (2017)
Allelic heterogeneity of albinism in the domestic cat.
GP00002313
Tyr
P11344
Morphology
c.1204C>T p.R402* N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase (TYR)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
Insertion
N
Bos taurus
cattle - (species) D
Domesticated
Candidate Gene
Schmutz SM; Berryere TG; Ciobanu DC ; et al. (2004)
A form of albinism in cattle is caused by a tyrosinase frameshift mutation.
GP00002315
Tyr
P11344
Morphology
c.925_926insC N
Bos taurus
cattle - (species)
Bos taurus
cattle - (species) D
tyrosinase (TYR)
Bos taurus
cattle - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Candidate Gene
Aigner B; Besenfelder U; Müller M ; et al. (2000)
Tyrosinase gene variants in different rabbit strains.
GP00002316
Tyr
P11344
Morphology
c.1118C>A p.T373K (also causes albinism in humans)
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
tyrosinase (TYR)
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Cavia porcellus
domestic guinea pig - (species) D
Domesticated
Candidate Gene
Yu F; Jiao S; Lai W ; et al. (2018)
Conserved aspartate-to-glycine mutation in tyrosinase is associated with albino phenotype in domesti[...]
GP00002317
Tyr
P11344
Morphology
c.710A>G p.Asp237Gly
Cavia porcellus
domestic guinea pig - (species)
Cavia porcellus
domestic guinea pig - (species) D
tyrosinase (TYR)
Cavia porcellus
domestic guinea pig - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Bubalus bubalis
water buffalo - (species) D
Domesticated
Candidate Gene
Damé MC; Xavier GM; Oliveira-Filho JP ; et al. (2012)
A nonsense mutation in the tyrosinase gene causes albinism in water buffalo.
GP00002318
Tyr
P11344
Morphology
c.1431G>A p.W477*
Bubalus bubalis
water buffalo - (species)
Bubalus bubalis
water buffalo - (species) D
tyrosinase (TYR)
Bubalus bubalis
water buffalo - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Neovison vison
American mink - (species) D
Domesticated
Candidate Gene
Anistoroaei R; Fredholm M; Christensen K ; et al. (2008)
Albinism in the American mink (Neovison vison) is associated with a tyrosinase nonsense mutation.
GP00002319
Tyr
P11344
Morphology
c.138T>A p.C46*
Neovison vison
American mink - (species)
Neovison vison
American mink - (species) D
tyrosinase (TYR)
Neovison vison
American mink - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (coat)
Coding,
SNP
Neovison vison
American mink - (species) D
Domesticated
Candidate Gene
Benkel BF; Rouvinen-Watt K; Farid H ; et al. (2009)
Molecular characterization of the Himalayan mink.
GP00002320
Tyr
P11344
Morphology
c.1835C>G p.H420Q
Neovison vison
American mink - (species)
Neovison vison
American mink - (species) D
tyrosinase (TYR)
Neovison vison
American mink - (species)
Published - Accepted by Curator
tyrosinase (TYR)
Coloration (amelanism)
Coding,
Insertion
N
Oryzias latipes
Japanese medaka - (species) D
Domesticated
Candidate Gene
Koga A; Hori H (1997)
Albinism due to transposable element insertion in fish.
GP00002372
Tyr
P11344
Morphology
"i4 allele was found to contain a 4.7- kb transposable element in the 5th exon"
"Tyr-i4 contains a 4.7-kb insertion in exon 5 (Fig. 3). If the inserted fragment was transcribed, the amino acid sequence would be altered after the 469th residue, with a termination codon (UAG) at amino acid position 471. The i4/i4 genotype exhibits a quasi-albino phenotype. This may be explained by generation of a tyrosinase protein that only lacks its C-terminus region. The wild-type tyrosinase has a highly hydrophobic amino acid block at its C terminus (aa 480 - aa 500) which is thought to be part of a membrane spanning domain (Inagaki et al., 1994). A possible explanation is that the mutant tyrosinase encoded by Tyr- i4 lacks this region, so that it cannot be positioned properly on the membrane" N
Oryzias latipes
Japanese medaka - (species)
Oryzias latipes
Japanese medaka - (species) D
tyrosinase (TYR)
Oryzias latipes
Japanese medaka - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
Bos taurus
cattle - (species)
Domesticated
Linkage Mapping
Berryere TG; Schmutz SM; Schimpf RJ ; et al. (2003)
TYRP1 is associated with dun coat colour in Dexter cattle or how now brown cow?
GP00001145
Tyrp1
P07147
Morphology
c.1300C>T p.H434Y
Bos taurus
cattle - (species)
Bos taurus
cattle - (species)
tyrosinase-related protein 1 (TYRP1)
Bos taurus
cattle - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
Deletion
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Schmutz SM; Berryere TG; Goldfinch AD (2002)
TYRP1 and MC1R genotypes and their effects on coat color in dogs.
GP00001146
Tyrp1
P07147
Morphology
deletion of a proline residue in exon 5 (345delP)
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
tyrosinase-related protein 1 (TYRP1)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Schmutz SM; Berryere TG; Goldfinch AD (2002)
TYRP1 and MC1R genotypes and their effects on coat color in dogs.
GP00001147
Tyrp1
P07147
Morphology
premature stop codon in exon 5 (Q331ter) N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
tyrosinase-related protein 1 (TYRP1)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (feathers)
Coding,
SNP
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014)
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
GP00001149
Tyrp1
P07147
Morphology
Ala23Pro
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
tyrosinase-related protein 1 (TYRP1)
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (feathers)
Coding,
SNP
N
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014)
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
GP00001150
Tyrp1
P07147
Morphology
Arg72* N
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
tyrosinase-related protein 1 (TYRP1)
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (feathers)
Coding,
Deletion
N
Columba livia
rock pigeon - (species) D
Domesticated
Linkage Mapping
Domyan ET; Guernsey MW; Kronenberg Z ; et al. (2014)
Epistatic and combinatorial effects of pigmentary gene mutations in the domestic pigeon.
GP00001151
Tyrp1
P07147
Morphology
7-bp deletion 411-418del resulting in null allele N
Columba livia
rock pigeon - (species)
Columba livia
rock pigeon - (species) D
tyrosinase-related protein 1 (TYRP1)
Columba livia
rock pigeon - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (feathers)
Coding,
SNP
Coturnix japonica
Japanese quail - (species)
Domesticated
Linkage Mapping
Nadeau NJ; Mundy NI; Gourichon D ; et al. (2007)
Association of a single-nucleotide substitution in TYRP1 with roux in Japanese quail (Coturnix japon[...]
GP00001152
Tyrp1
P07147
Morphology
Phe282Ser
Coturnix japonica
Japanese quail - (species)
Coturnix japonica
Japanese quail - (species)
tyrosinase-related protein 1 (TYRP1)
Coturnix japonica
Japanese quail - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
N
Felis catus
domestic cat - (species) D
Domesticated
Linkage Mapping
Schmidt-Küntzel A; Eizirik E; O'Brien SJ ; et al. (2005 Jul-Aug)
Tyrosinase and tyrosinase related protein 1 alleles specify domestic cat coat color phenotypes of th[...]
1 Additional References
GP00001153
Tyrp1
P07147
Morphology
premature UAG stop codon at position 100 of TYRP1; AAG>TAG c.298C>T p.R100* N
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase-related protein 1 (TYRP1)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
Unknown
Felis catus
domestic cat - (species) D
Domesticated
Linkage Mapping
Schmidt-Küntzel A; Eizirik E; O'Brien SJ ; et al. (2005 Jul-Aug)
Tyrosinase and tyrosinase related protein 1 alleles specify domestic cat coat color phenotypes of th[...]
GP00001154
Tyrp1
P07147
Morphology
Two mutations associated with the chocolate (b) allele - one leading to a TYRP1-A3G substitution in the signal peptide and another to an in-frame insertion TYRP1-421ins17/18 caused by a donor splice site mutation in intron 6 -exact causing change unknown
Felis catus
domestic cat - (species)
Felis catus
domestic cat - (species) D
tyrosinase-related protein 1 (TYRP1)
Felis catus
domestic cat - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Gratten J; Beraldi D; Lowder BV ; et al. (2007)
Compelling evidence that a single nucleotide substitution in TYRP1 is responsible for coat-colour po[...]
GP00001156
Tyrp1
P07147
Morphology
c. 869G>T p.C290F ; Cys residue involved shows a high degree of evolutionary conservation; it is conserved not only across vertebrates but also in the two paralogues of TYRP1, DCT and TYR
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
tyrosinase-related protein 1 (TYRP1)
Ovis aries
sheep - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
Deletion
Sus scrofa domesticus
domestic pig - (subspecies) D
Domesticated
Candidate Gene
Wu X; Zhang Y; Shen L ; et al. (2016)
A 6-bp deletion in exon 8 and two mutations in introns of TYRP1 are associated with blond coat color[...]
GP00001327
Tyrp1
P07147
Morphology
g.17599_17604del 6bp deletion in exon 8 resulting in deletion of Met and Gly residues at positions 495 and 496 in TYRP1 protein ; c.1484_1489del6 p.Met495_Gly496del
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies) D
tyrosinase-related protein 1 (TYRP1)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (feathers)
Coding,
SNP
Gallus gallus
chicken - (species)
Domesticated
Linkage Mapping
Li J; Bed'hom B; Marthey S ; et al. (2019)
A missense mutation in TYRP1 causes the chocolate plumage color in chicken and alters melanosome str[...]
GP00002126
Tyrp1
P07147
Morphology
g.30830367C>A c.640C>A p.His214Asn
Gallus gallus
chicken - (species)
Gallus gallus
chicken - (species)
tyrosinase-related protein 1 (TYRP1)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Schmutz SM; Berryere TG; Goldfinch AD (2002)
TYRP1 and MC1R genotypes and their effects on coat color in dogs.
GP00002233
Tyrp1
P07147
Morphology
c.121T>A p.Cys41Ser
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
tyrosinase-related protein 1 (TYRP1)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
N
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Hrckova Turnova E; Majchrakova Z; Bielikova M ; et al. (2017)
A novel mutation in the TYRP1 gene associated with brown coat colour in the Australian Shepherd Dog [...]
GP00002234
Tyrp1
P07147
Morphology
c.555T>G p.Tyr185* N
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
tyrosinase-related protein 1 (TYRP1)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
Canis lupus familiaris
dog - (subspecies) D
Domesticated
Candidate Gene
Wright HE; Schofield E; Mellersh CS ; et al. (2019)
A novel TYRP1 variant is associated with liver and tan coat colour in Lancashire Heelers.
GP00002235
Tyrp1
P07147
Morphology
c.1025T>G p.Phe342Cys
Canis lupus
gray wolf - (species)
Canis lupus familiaris
dog - (subspecies) D
tyrosinase-related protein 1 (TYRP1)
Canis lupus familiaris
dog - (subspecies)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
Capra hircus
goat - (species) D
Domesticated
Candidate Gene
Becker D; Otto M; Ammann P ; et al. (2015)
The brown coat colour of Coppernecked goats is associated with a non-synonymous variant at the TYRP1[...]
GP00002236
Tyrp1
P07147
Morphology
c.1487G>A p.Gly496Asp
Capra hircus
goat - (species)
Capra hircus
goat - (species) D
tyrosinase-related protein 1 (TYRP1)
Capra hircus
goat - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Raadsma HW; Jonas E; Fleet MR ; et al. (2013)
QTL and association analysis for skin and fibre pigmentation in sheep provides evidence of a major c[...]
GP00002237
Tyrp1
P07147
Morphology
c.2240C>G p.A746V
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
tyrosinase-related protein 1 (TYRP1)
Ovis aries
sheep - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
Deletion
N
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Paris JM; Letko A; Häfliger IM ; et al. (2019)
Identification of two TYRP1 loss-of-function alleles in Valais Red sheep.
GP00002238
Tyrp1
P07147
Morphology
c.86_87delGA p.(Glu29ValfsTer5) N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
tyrosinase-related protein 1 (TYRP1)
Ovis aries
sheep - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
N
Ovis aries
sheep - (species) D
Domesticated
Linkage Mapping
Paris JM; Letko A; Häfliger IM ; et al. (2019)
Identification of two TYRP1 loss-of-function alleles in Valais Red sheep.
GP00002239
Tyrp1
P07147
Morphology
c.1066C>T p.(Arg356*) N
Ovis aries
sheep - (species)
Ovis aries
sheep - (species) D
tyrosinase-related protein 1 (TYRP1)
Ovis aries
sheep - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Coding,
SNP
N
Oryctolagus cuniculus
rabbit - (species) D
Domesticated
Linkage Mapping
Utzeri VJ; Ribani A; Fontanesi L (2014)
A premature stop codon in the TYRP1 gene is associated with brown coat colour in the European rabbit[...]
GP00002240
Tyrp1
P07147
Morphology
c.570G>A p.Trp190ter N
Oryctolagus cuniculus
rabbit - (species)
Oryctolagus cuniculus
rabbit - (species) D
tyrosinase-related protein 1 (TYRP1)
Oryctolagus cuniculus
rabbit - (species)
Published - Accepted by Curator
tyrosinase-related protein 1 (TYRP1)
Coloration (coat)
Cis-regulatory,
Insertion
N
Neovison vison
American mink - (species) D
Domesticated
Candidate Gene
Cirera S; Markakis MN; Kristiansen T ; et al. (2016)
A large insertion in intron 2 of the TYRP1 gene associated with American Palomino phenotype in Ameri[...]
GP00002241
Tyrp1
P07147
Morphology
Large insertion in intron 2 resulting in aberrant transcript N
Neovison vison
American mink - (species)
Neovison vison
American mink - (species) D
tyrosinase-related protein 1 (TYRP1)
Neovison vison
American mink - (species)
Published - Accepted by Curator
Tyrosine hydroxylase
Coloration (body)
Cis-regulatory,
Unknown
Bombyx mori
domestic silkworm - (species) D
Domesticated
Candidate Gene
Yu HS; Shen YH; Yuan GX ; et al. (2011)
Evidence of selection at melanin synthesis pathway loci during silkworm domestication.
GP00001158
ple
P18459
Morphology
Variation in intron; possibly loss of AbdA binding site
Bombyx mandarina
wild silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Tyrosine hydroxylase
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
UGT86 (Bm-UGT10286)
Coloration (cocoon)
Gene Loss,
Deletion
N
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Daimon T; Hirayama C; Kanai M ; et al. (2010)
The silkworm Green b locus encodes a quercetin 5-O-glucosyltransferase that produces green cocoons w[...]
1 Additional References
GP00001160
Bm-UGT10286
D6RUU6
Physiology
38kb gene deletion N
Bombyx
(genus)
Bombyx mori
domestic silkworm - (species) D
UGT86 (Bm-UGT10286)
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
Vertnin (VRTN)
Vertebrae number
Cis-regulatory,
Unknown
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Mikawa S; Sato S; Nii M ; et al. (2011)
Identification of a second gene associated with variation in vertebral number in domestic pigs.
GP00001165
Vrtn
Q3SYK4
Morphology
unknown ; observed transposon insertion in intron and promoter variation
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
Vertnin (VRTN)
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
Vertnin (VRTN) [possibly a pseudo-replicate of other Pig entry]
Vertebrae number
Unknown,
Unknown
Sus scrofa domesticus
domestic pig - (subspecies)
Domesticated
Linkage Mapping
Ren DR; Ren J; Ruan GF ; et al. (2012)
Mapping and fine mapping of quantitative trait loci for the number of vertebrae in a White Duroc × C[...]
GP00001166
Vrtn
Q3SYK4
Morphology
unknown
Sus scrofa
pig - (species)
Sus scrofa domesticus
domestic pig - (subspecies)
Vertnin (VRTN) [possibly a pseudo-replicate of other Pig entry]
Sus scrofa domesticus
domestic pig - (subspecies)
Published - Accepted by Curator
VPS13A
Latitudinal adaptation
Coding,
SNP
Sus scrofa
pig - (species) D
Domesticated
Association Mapping
Ai H; Fang X; Yang B ; et al. (2015)
Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequen[...]
GP00001571
VPS13A
F1SIL5
Physiology
two nonsynonymous substitutions V>G and F>Y - whether both or only one affects the phenotype is unknown
Sus scrofa
pig - (species)
Sus scrofa
pig - (species) D
VPS13A
Sus scrofa
pig - (species)
Published - Accepted by Curator
VRN1
Flowering time
Cis-regulatory,
Deletion
Triticum aestivum
bread wheat - (species) D
Domesticated
Linkage Mapping
Trevaskis B; Bagnall DJ; Ellis MH ; et al. (2003)
MADS box genes control vernalization-induced flowering in cereals.
GP00001184
VRN1
Q8L3W1
Physiology
Deletion
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species) D
VRN1
Triticum aestivum
bread wheat - (species)
Published - Accepted by Curator
VRN1
Flowering time
Cis-regulatory,
Unknown
Triticum monococcum
(species)
Domesticated
Linkage Mapping
Yan L; Loukoianov A; Tranquilli G ; et al. (2003)
Positional cloning of the wheat vernalization gene VRN1.
GP00001185
VRN1
Q8L3W1
Physiology
Not identified
Triticum monococcum
(species)
Triticum monococcum
(species)
VRN1
Triticum monococcum
(species)
Published - Accepted by Curator
VRN1
Flowering time
Cis-regulatory,
Insertion
Triticum turgidum
(species) D
Domesticated
Linkage Mapping
Chu CG; Tan CT; Yu GT ; et al. (2011)
A Novel Retrotransposon Inserted in the Dominant Vrn-B1 Allele Confers Spring Growth Habit in Tetrap[...]
GP00002105
VRN1
Q8L3W1
Physiology
5463-bp insertion in the 5'-UTR region of the Vrn-B1 allele. This insertion is a novel retrotransposon (designated as retrotrans_VRN), which is flanked by a 5-bp target site duplication and contains primer binding site and polypurine tract motifs; a 325-bp long terminal repeat and an open reading frame encoding 1231 amino acids. The insertion of retrotrans_VRN results in expression of Vrn-B1 without vernalization.
Triticum turgidum
(species)
Triticum turgidum
(species) D
VRN1
Triticum turgidum
(species)
Published - Accepted by Curator
VRN2
Flowering time
Gene Loss,
Deletion
N
Hordeum vulgare
(species)
Domesticated
Linkage Mapping
Yan L; Loukoianov A; Blechl A ; et al. (2004)
The wheat VRN2 gene is a flowering repressor down-regulated by vernalization.
GP00001186
VRN2
Q8W5B1
Physiology
Large deletion N
Hordeum vulgare
(species)
Hordeum vulgare
(species)
VRN2
Hordeum vulgare
(species)
Published - Accepted by Curator
VRN2
Flowering time
Coding,
SNP
Triticum monococcum
(species)
Domesticated
Linkage Mapping
Yan L; Loukoianov A; Blechl A ; et al. (2004)
The wheat VRN2 gene is a flowering repressor down-regulated by vernalization.
GP00001187
VRN2
Q8W5B1
Physiology
R35W; R is conserved in all of the ZCCT proteins and in all of the CO-like proteins from Arabidopsis; rice; and barley
Triticum monococcum
(species)
Triticum monococcum
(species)
VRN2
Triticum monococcum
(species)
Published - Accepted by Curator
VRN2
Flowering time
Gene Loss,
Deletion
N
Triticum monococcum
(species) D
Domesticated
Candidate Gene
Yan L; Loukoianov A; Blechl A ; et al. (2004)
The wheat VRN2 gene is a flowering repressor down-regulated by vernalization.
GP00001188
VRN2
Q8W5B1
Physiology
Large deletion; complete deletion of ZCCT1 and ZCCT2=VRN2 genes N
Triticum monococcum
(species)
Triticum monococcum
(species) D
VRN2
Triticum monococcum
(species)
Published - Accepted by Curator
VRS1 = SIX-ROWED SPIKE 1
Plant architecture
Inflorescence architecture
Coding,
Deletion
N
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Komatsuda T; Pourkheirandish M; He C ; et al. (2007)
Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene.
1 Additional References
GP00001189
Vrs1
A1IHK8
Morphology
Morphology
1bp deletion resulting in frameshift N
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
VRS1 = SIX-ROWED SPIKE 1
Hordeum vulgare
(species)
Published - Accepted by Curator
VRS1 = SIX-ROWED SPIKE 1
Plant architecture
Inflorescence architecture
Coding,
Insertion
N
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Komatsuda T; Pourkheirandish M; He C ; et al. (2007)
Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene.
1 Additional References
GP00001190
Vrs1
A1IHK8
Morphology
Morphology
1bp insertion resulting in frameshift N
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
VRS1 = SIX-ROWED SPIKE 1
Hordeum vulgare
(species)
Published - Accepted by Curator
VRS1 = SIX-ROWED SPIKE 1
Plant architecture
Inflorescence architecture
Coding,
SNP
Hordeum vulgare
(species)
Domesticated
Linkage Mapping
Komatsuda T; Pourkheirandish M; He C ; et al. (2007)
Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene.
1 Additional References
GP00001191
Vrs1
A1IHK8
Morphology
Morphology
Phe75Leu
Hordeum vulgare
(species)
Hordeum vulgare
(species)
VRS1 = SIX-ROWED SPIKE 1
Hordeum vulgare
(species)
Published - Accepted by Curator
VTE3(1)
Vitamin-E synthesis
Cis-regulatory,
Epigenetic Change
Solanum lycopersicum
tomato - (species)
Domesticated
Linkage Mapping
Quadrana L; Almeida J; Asís R ; et al. (2014)
Natural occurring epialleles determine vitamin E accumulation in tomato fruits.
GP00001684
VTE3
Q9LY74
Physiology
Solanum lycopersicum
tomato - (species)
Solanum lycopersicum
tomato - (species)
VTE3(1)
Solanum lycopersicum
tomato - (species)
Published - Accepted by Curator
VvMYBA1
Coloration (fruit)
Cis-regulatory,
Insertion
Vitis vinifera
wine grape - (species) D
Domesticated
Candidate Gene
Kobayashi S; Goto-Yamamoto N; Hirochika H (2004)
Retrotransposon-induced mutations in grape skin color.
GP00001192
VvmybA1
Q6L973
Morphology
Gret1 retrotransposon insertion
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMYBA1
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA1
Coloration (fruit)
Unknown,
Unknown
Vitis vinifera
wine grape - (species)
Domesticated
Linkage Mapping
Fournier-Level A; Le Cunff L; Gomez C ; et al. (2009)
Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp. sativa) berry: [...]
GP00001193
VvmybA1
Q6L973
Morphology
Gret1 insertion polymorphism + R188S + Q213P
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species)
VvMYBA1
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA1
Coloration (fruit)
Cis-regulatory,
Deletion
Vitis vinifera
wine grape - (species) D
Domesticated
Candidate Gene
Kobayashi S; Goto-Yamamoto N; Hirochika H (2004)
Retrotransposon-induced mutations in grape skin color.
1 Additional References
GP00001194
VvmybA1
Q6L973
Morphology
Gret1 retrotransposon deletion; leaving behind its 3'-LTR flanked by 5 bp of a duplicated target site
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMYBA1
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA1
Coloration (fruit)
Cis-regulatory,
Deletion
Vitis vinifera
wine grape - (species) D
Domesticated
Candidate Gene
Ferreira V; Matus JT; Pinto-Carnide O ; et al. (2019)
Genetic analysis of a white-to-red berry skin color reversion and its transcriptomic and metabolic c[...]
GP00002096
VvmybA1
Q6L973
Morphology
partial excision of the Gret1 retrotransposon from the promoter region of the MYBA1 anthocyanin regulator - associated with white-to-red berry skin color reversion
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMYBA1
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA1
Coloration (fruit)
Cis-regulatory,
Insertion
Vitis vinifera
wine grape - (species) D
Domesticated
Candidate Gene
Shimazaki M; Fujita K; Kobayashi H ; et al. (2011)
Pink-colored grape berry is the result of short insertion in intron of color regulatory gene.
GP00002097
VvmybA1
Q6L973
Morphology
33 bp insertion in the second intron of the MYBA1 red allele which affects messenger RNA (mRNA) stability - 16 bp of the 3' end in the insertion is a key structure for a defect in splicing of MybA1 transcripts
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMYBA1
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA1
Coloration (fruit)
Other,
Deletion
Vitis vinifera
wine grape - (species) D
Domesticated
Candidate Gene
Azuma A; Kobayashi S; Goto-Yamamoto N ; et al. (2009)
Color recovery in berries of grape (Vitis vinifera L.) 'Benitaka', a bud sport of 'Italia', is cause[...]
GP00002099
VvmybA1
Q6L973
Morphology
homologous recombination between the non-functional allele of MybA1 and the truncated MybA3 gene at their promoter region, resulting in the recovery of MybA1 genomic integrity (and therefore its transcription) on cv. ‘Benitaka’. The VvmybA1 locus of 'Benitaka' is heterozygous for the VvmybA1a allele (non-functional) and a novel VvmybA1(BEN) allele. VvmybA1(BEN) restores VvmybA1 transcripts.
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMYBA1
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMybA1 VvMybA2 VvMybA3 and VvMybA4
Coloration (fruit)
Gene Loss,
Complex Change
N
Vitis vinifera
wine grape - (species) D
Domesticated
Candidate Gene
Carbonell-Bejerano P; Royo C; Torres-Pérez R ; et al. (2017)
Catastrophic Unbalanced Genome Rearrangements Cause Somatic Loss of Berry Color in Grapevine.
GP00002098
VvmybA3
Q6L9M7
Morphology
catastrophic genome rearrangement: intrachromosomal and interchromosomal translocations and the deletion of 313 genes including the loss of the functional copy for the MYB transcription factors required for anthocyanin pigmentation in the berry skin N
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMybA1 VvMybA2 VvMybA3 and VvMybA4
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA2
Coloration (fruit)
2 Mutations:
Coding
N
Vitis vinifera
wine grape - (species) D
Domesticated
Linkage Mapping
Fournier-Level A; Le Cunff L; Gomez C ; et al. (2009)
Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp. sativa) berry: [...]
GP00001195
VvmybA2
Q6L9M8
Morphology
2 mutations
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species) D
VvMYBA2
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
VvMYBA3
Coloration (fruit)
Cis-regulatory,
SNP
Vitis vinifera
wine grape - (species)
Domesticated
Linkage Mapping
Fournier-Level A; Le Cunff L; Gomez C ; et al. (2009)
Quantitative genetic bases of anthocyanin variation in grape (Vitis vinifera L. ssp. sativa) berry: [...]
GP00001196
VvmybA3
Q6L9M7
Morphology
Substitution in promoter
Vitis vinifera
wine grape - (species)
Vitis vinifera
wine grape - (species)
VvMYBA3
Vitis vinifera
wine grape - (species)
Published - Accepted by Curator
Waxy /GBSS
Amylose content
Cis-regulatory,
Deletion
Hordeum vulgare
(species) D
Domesticated
Linkage Mapping
Domon E; Fuijita M; Ishikawa N (2002)
The insertion/deletion polymorphisms in the waxy gene of barley genetic resources from East Asia.
GP00001197
waxy
Q8L699
Physiology
403-bp deletion spanning from position –129 bp to position +274 relative to the deduced starting point of transcription in the barley waxy gene and
Hordeum vulgare
(species)
Hordeum vulgare
(species) D
Waxy /GBSS
Hordeum vulgare
(species)
Published - Accepted by Curator
Waxy /GBSS
Amylose content
Cis-regulatory,
Insertion
Setaria italica
foxtail millet - (species) D
Domesticated
Candidate Gene
Kawase M; Fukunaga K; Kato K (2005)
Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transpo[...]
GP00001198
waxy
Q8L699
Physiology
Transposon insertion TSI-11 (Intron 12)
Setaria italica
foxtail millet - (species)
Setaria italica
foxtail millet - (species) D
Waxy /GBSS
Setaria italica
foxtail millet - (species)
Published - Accepted by Curator
Waxy /GBSS
Amylose content
Cis-regulatory,
Insertion
Setaria italica
foxtail millet - (species) D
Domesticated
Linkage Mapping
Kawase M; Fukunaga K; Kato K (2005)
Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transpo[...]
GP00001199
waxy
Q8L699
Physiology
Transposon insertion TSI-2 (intron 1)
Setaria italica
foxtail millet - (species)
Setaria italica
foxtail millet - (species) D
Waxy /GBSS
Setaria italica
foxtail millet - (species)
Published - Accepted by Curator
Waxy /GBSS
Amylose content
Cis-regulatory,
Insertion
Setaria italica
foxtail millet - (species) D
Domesticated
Candidate Gene
Kawase M; Fukunaga K; Kato K (2005)
Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transpo[...]
GP00001200
waxy
Q8L699
Physiology
Transposon insertion TSI-10 (Intron 12)
Setaria italica
foxtail millet - (species)
Setaria italica
foxtail millet - (species) D
Waxy /GBSS
Setaria italica
foxtail millet - (species)
Published - Accepted by Curator
Waxy /GBSS
Amylose content
Coding,
Insertion
N
Setaria italica
foxtail millet - (species) D
Domesticated
Candidate Gene
Kawase M; Fukunaga K; Kato K (2005)
Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transpo[...]
GP00001201
waxy
Q8L699
Physiology
Transposon insertion TS1-7 (Exon 3) N
Setaria italica
foxtail millet - (species)
Setaria italica
foxtail millet - (species) D
Waxy /GBSS
Setaria italica
foxtail millet - (species)
Published - Accepted by Curator
Waxy /GBSS
Amylose content
Coding,
Insertion
N
Setaria italica
foxtail millet - (species) D
Domesticated
Candidate Gene
Kawase M; Fukunaga K; Kato K (2005)
Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transpo[...]
GP00001202
waxy
Q8L699
Physiology
Transposon insertion TS1-9 (Exon 10) N
Setaria italica
foxtail millet - (species)
Setaria italica
foxtail millet - (species) D
Waxy /GBSS
Setaria italica
foxtail millet - (species)
Published - Accepted by Curator
Waxy /GBSS
Amylose content
Cis-regulatory,
Deletion
Setaria italica
foxtail millet - (species) D
Domesticated
Candidate Gene
Kawase M; Fukunaga K; Kato K (2005)
Diverse origins of waxy foxtail millet crops in East and Southeast Asia mediated by multiple transpo[...]
GP00001203
waxy
Q8L699
Physiology
2.4kb deletion (intron 1)
Setaria italica
foxtail millet - (species)
Setaria italica
foxtail millet - (species) D
Waxy /GBSS
Setaria italica
foxtail millet - (species)
Published - Accepted by Curator
Waxy /GBSS
Amylose content (glutinous rice)
Coding,
SNP
Oryza sativa
rice - (species)
Domesticated
Linkage Mapping
Wang ZY; Zheng FQ; Shen GZ ; et al. (1995)
The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy [...]
3 Additional References
GP00001204
waxy
Q8L699
Physiology
substitution G->T in the 5' splice site of intron 1
Oryza sativa
rice - (species)
Oryza sativa
rice - (species)
Waxy /GBSS
Oryza sativa
rice - (species)
Published - Accepted by Curator
Waxy /GBSS
Amylose content (glutinous rice)
Coding,
Insertion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Hori Y; Fujimoto R; Sato Y ; et al. (2007)
A novel wx mutation caused by insertion of a retrotransposon-like sequence in a glutinous cultivar o[...]
GP00002069
waxy
Q8L699
Physiology
23-bp duplication in the second exon which causes loss of the function of granule-bound starch synthase (GBSS) encoded by the Wx gene N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Waxy /GBSS
Oryza sativa
rice - (species)
Published - Accepted by Curator
Waxy /GBSS
Amylose content (glutinous rice)
Coding,
Insertion
N
Oryza sativa
rice - (species) D
Domesticated
Candidate Gene
Hori Y; Fujimoto R; Sato Y ; et al. (2007)
A novel wx mutation caused by insertion of a retrotransposon-like sequence in a glutinous cultivar o[...]
GP00002070
waxy
Q8L699
Physiology
insertion of 7764 bp in the ninth exon of the wx gene. Transcripts of the 'Oragamochi' wx allele are about 1-kb shorter and the deduced amino acid sequence of the transcript lacks a motif important for GBSS. The 7,764-bp insertion is a retrotransposon-like sequence with long terminal repeats; a primer binding site and a polypurine tract N
Oryza sativa
rice - (species)
Oryza sativa
rice - (species) D
Waxy /GBSS
Oryza sativa
rice - (species)
Published - Accepted by Curator
WDR1
Coloration (flowers; seeds; stems)
Coding,
Deletion
N
Ipomoea nil
Japanese morning glory - (species) D
Domesticated
Candidate Gene
Morita Y; Saitoh M; Hoshino A ; et al. (2006)
Isolation of cDNAs for R2R3-MYB, bHLH and WDR transcriptional regulators and identification of c and[...]
GP00002090
InWDR1
Q1JUZ7
Morphology
frameshift mutation caused by a 7 bp insertion in the gene encoding a WDR transcriptional regulator N
Ipomoea nil
Japanese morning glory - (species)
Ipomoea nil
Japanese morning glory - (species) D
WDR1
Ipomoea nil
Japanese morning glory - (species)
Published - Accepted by Curator
WDR1
Coloration (flowers)
Coding,
Insertion
N
Petunia axillaris
(species) D
Domesticated
Candidate Gene
de Vetten N; Quattrocchio F; Mol J ; et al. (1997)
The an11 locus controlling flower pigmentation in petunia encodes a novel WD-repeat protein conserve[...]
GP00002093
InWDR1
Q1JUZ7
Morphology
insertion of a 300-bp dTph1 transposon in the WDR gene in the first WD-repeat (321-bp downstream of the transcription start site) N
Petunia axillaris
(species)
Petunia axillaris
(species) D
WDR1
Petunia axillaris
(species)
Published - Accepted by Curator
WIF1
Ear size
Coding,
SNP
Sus scrofa
pig - (species) D
Domesticated
Candidate Gene
Liang J; Zhang Y; Wang L ; et al. (2019)
Molecular cloning of WIF1 and HMGA2 reveals ear-preferential expression while uncovering a missense [...]
GP00002255
WIF1
Q9Y5W5
Morphology
p.Phe236Leu
Sus scrofa
pig - (species)
Sus scrofa
pig - (species) D
WIF1
Sus scrofa
pig - (species)
Published - Accepted by Curator
Wnt receptor
Fin morphology (skeleton; dorsal fin)
Cis-regulatory,
Unknown
Carassius auratus
goldfish - (species) D
Domesticated
Association Mapping
Kon T; Omori Y; Fukuta K ; et al. (2020)
The Genetic Basis of Morphological Diversity in Domesticated Goldfish.
GP00002347
Lrp6
O88572
Morphology
Lrp6 gene expression is reduced in goldfish with the dorsal fin loss phenotype. Only four amino acid substitutions in the coding region and all of them are conserved or semi-conserved in zebrafish or medaka lrp6 orthologs. There is a 313-bp deletion in intron 21 of lrp6S in goldfish with the dorsal fin loss phenotype. This intronic deletion may affect induction and proper production of lrp6S mRNA at embryonic stages.
Carassius auratus
goldfish - (species)
Carassius auratus
goldfish - (species) D
Wnt receptor
Carassius auratus
goldfish - (species)
Published - Accepted by Curator
Wnt1
Coloration (larval color pattern)
Cis-regulatory,
Complex Change
Bombyx mori
domestic silkworm - (species) D
Domesticated
Linkage Mapping
Yamaguchi J; Banno Y; Mita K ; et al. (2013)
Periodic Wnt1 expression in response to ecdysteroid generates twin-spot markings on caterpillars.
2 Additional References
GP00001385
wg
P09615
Morphology
Fine-resolution mapping of a 34kb regulatory region driving Ecdysteroid-dependent Wnt gain-of-function. The L-specific structural variations upstream of Wnt1-1 may cause its ectopic expression in the spot marking region of the epidermis, resulting in the L phenotype.
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Wnt1
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
Wnt1
Coloration (larval color pattern)
Cis-regulatory,
Deletion
Bombyx mori
domestic silkworm - (species) D
Domesticated
Association Mapping
Tong X; Han MJ; Lu K ; et al. (2022)
High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecologic[...]
GP00002403
wg
P09615
Morphology
A specific large deletion (271 kb) is present in the 3′-flanking region of Wnt1. Wnt1 expression is significantly higher in the epidermis of heterozygous LC (LC/+) mutants than in normal strains (+/+).
Bombyx mori
domestic silkworm - (species)
Bombyx mori
domestic silkworm - (species) D
Wnt1
Bombyx mori
domestic silkworm - (species)
Published - Accepted by Curator
Y
Coloration (fruit)
Coding,
Insertion
Sorghum bicolor
sorghum - (species) D
Domesticated
Candidate Gene
Chopra S; Brendel V; Zhang J ; et al. (1999)
Molecular characterization of a mutable pigmentation phenotype and isolation of the first active tra[...]
GP00002068
P1
O24579
Morphology
insertion of a transposable element named Candystripe1 (Cs1) in the second intron of the Y gene - Cs1 is 23,018 bp in size and is bordered by 20-bp terminal inverted repeat sequences. It generated a 3-bp target site duplication upon insertion within the Y gene. Cs1 shares features of the CACTA superfamily of transposons.
Sorghum bicolor
sorghum - (species)
Sorghum bicolor
sorghum - (species) D
Y
Sorghum bicolor
sorghum - (species)
Published - Accepted by Curator
zfl2
Flowering time
Coding,
Deletion
Zea mays
(species) D
Domesticated
Linkage Mapping
Buckler ES; Holland JB; Bradbury PJ ; et al. (2009)
The genetic architecture of maize flowering time.
GP00001226
zfl2
Q5Q1L6
Physiology
16a.a. deletion
Zea mays
(species)
Zea mays
(species) D
zfl2
Zea mays
(species)
Published - Accepted by Curator
zic1/zic4
Fin morphology (skeleton; caudal fin)
Cis-regulatory,
Deletion
Betta splendens
Siamese fighting fish - (species) D
Domesticated
Linkage Mapping
Wang L; Sun F; Wan ZY ; et al. (2021)
Genomic Basis of Striking Fin Shapes and Colors in the Fighting Fish.
GP00002385
Zic1
P46684
Morphology
"We further sequenced the genomes of both homozygous single- and double-tail fish and found in double tail no large sequence variation except for a ∼180-bp deletion ∼15-kb downstream of zic4 (fig. 4C and supplementary fig. S19a, Supplementary Material online). This deletion was located in a cluster of CNEs and coincided with predicted CNE.006008 (supplementary fig. S19b, Supplementary Material online)."
"We observed that the wild-type ST allele significantly enhanced green fluorescent protein (GFP) expression in embryos at 24 hpf, when both zic1 and zic4 show differential expression between double-tail and wild-type fish (Moriyama et al. 2012), whereas no visible GFP expression was detected for the st allele (fig. 4E and supplementary table S11, Supplementary Material online). The efficiency of the two alleles as candidate enhancers was further examined using a Dual-Luciferase Reporter Assay, which showed that the ST allele enhanced luciferase expression by ∼10× relative to st allele in Singapore grouper embryonic cell line (fig. 4F)."
"Finally, we deleted this enhancer using the CRISPR-Cas9 system in fighting fish. Considering the efficiency of tested gRNAs and the cluster of CNEs that could have unpredicted functions, we limited the modification to the CNE.006008 region and did not involve the other CNEs (supplementary fig. S20, Supplementary Material online). Genetic analysis revealed that none of these fish had completely deleted CNE.006008, suggesting nonsimultaneous cutting at multiple targeted gRNA positions. These mosaic fish (n = 7) had significantly more fin rays than the noninjected controls (P < 0.01; fig. 4G). "
Betta splendens
Siamese fighting fish - (species)
Betta splendens
Siamese fighting fish - (species) D
zic1/zic4
Betta splendens
Siamese fighting fish - (species)
Published - Accepted by Curator
ZmCCT
Flowering time
Cis-regulatory,
Insertion
Zea mays
(species) D
Domesticated
Linkage Mapping
Ducrocq S; Giauffret C; Madur D ; et al. (2009)
Fine mapping and haplotype structure analysis of a major flowering time quantitative trait locus on [...]
2 Additional References
GP00001227
GHD7
E5RQA1
Physiology
insertion of a CACTA-like transposon into the promoter of ZmCCT. This insertion suppresses ZmCCT expression through methylation and reduces maize sensitivity to photoperiod.
Zea mays
(species)
Zea mays
(species) D
ZmCCT
Zea mays
(species)
Published - Accepted by Curator
ZmNAC111
Drought tolerance
Cis-regulatory,
Insertion
N
Zea mays
(species) D
Domesticated
Association Mapping
Yang Q; Li Z; Li W ; et al. (2013)
CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the post[...]
GP00002084
Morphology; Physiology
MITE insertion within the ZmCCT promoter which results in histone hypermethylation and represses the expression of NAC; resulting in a higher drought tolerance. N
Zea mays
(species)
Zea mays
(species) D
ZmNAC111
Zea mays
(species)
Published - Accepted by Curator