ABCA2
Xenobiotic resistance (insecticide; Bt Cry2Ab toxin)
Coding,
Indel
N
Helicoverpa armigera
cotton bollworm - (species) D
Intraspecific
Linkage Mapping
Tay WT; Mahon RJ; Heckel DG ; et al. (2015)
Insect Resistance to Bacillus thuringiensis Toxin Cry2Ab Is Conferred by Mutations in an ABC Transpo[...]
GP00000002
ABCA2
A0A0S0G7V0
Physiology
65bp indel in exon16 inducing a frameshift N
Helicoverpa armigera
cotton bollworm - (species)
Helicoverpa armigera
cotton bollworm - (species) D
ABCA2
Helicoverpa armigera
cotton bollworm - (species)
Published - Accepted by Curator
achaete-scute complex
Bristle number (abdomen)
Cis-regulatory,
Indel
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Long AD; Lyman RF; Morgan AH ; et al. (2000)
Both naturally occurring insertions of transposable elements and intermediate frequency polymorphism[...]
GP00000047
sc
P10084
Morphology
indel MC21 in promoter region of scute
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
achaete-scute complex
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
achaete-scute complex
Bristle number (thorax)
Cis-regulatory,
Indel
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Linkage Mapping
Gruber JD; Genissel A; Macdonald SJ ; et al. (2007)
How repeatable are associations between polymorphisms in achaete-scute and bristle number variation [...]
GP00000048
sc
P10084
Morphology
indel MC22 in promoter region of scute
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
achaete-scute complex
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
alcohol dehydrogenase (Adh)
Xenobiotic resistance (alcohol)
6 Mutations:
Drosophila melanogaster
fruit fly - (species) D
Intraspecific
Linkage Mapping
Choudhary M; Laurie CC (1991)
Use of in vitro mutagenesis to analyze the molecular basis of the difference in Adh expression assoc[...]
4 Additional References
GP00001962
Adh
P00334
Physiology
6 mutations
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species) D
alcohol dehydrogenase (Adh)
Drosophila melanogaster
fruit fly - (species)
Published - Accepted by Curator
Allantoin permease DAL4
Nitrogen use (growth rate on allantoin)
Coding,
Indel
N
Saccharomyces cerevisiae
baker's yeast - (species) D
Intraspecific
Linkage Mapping
Ibstedt S; Stenberg S; Bagés S ; et al. (2015)
Concerted evolution of life stage performances signals recent selection on yeast nitrogen use.
GP00001503
DAL4
Q04895
Physiology
c.1201delA a single nucleotide frameshifting insertion (deletion?) N
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species) D
Allantoin permease DAL4
Saccharomyces cerevisiae
baker's yeast - (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
amelogenin (AMEL)
Tooth absence (no enamel production)
3 Mutations:
Coding
N
Gallus gallus
chicken - (species) D
Intergeneric or Higher
Candidate Gene
Sire JY; Delgado SC; Girondot M (2008)
Hen's teeth with enamel cap: from dream to impossibility.
GP00001933
Amelx
P63277
Physiology
3 mutations
Paleosuchus palpebrosus
Cuvier's dwarf caiman - (species)
Gallus gallus
chicken - (species) D
amelogenin (AMEL)
Gallus gallus
chicken - (species)
Published - Accepted by Curator
CCL3L1
Pathogen resistance (HIV)
Gene Amplification,
Indel
Homo sapiens
human - (species) D
Intraspecific
Candidate Gene
Gonzalez E; Kulkarni H; Bolivar H ; et al. (2005)
The influence of CCL3L1 gene-containing segmental duplications on HIV-1/AIDS susceptibility.
GP00000177
CCL3L1
P16619
Physiology
Copy number Variant
Homo sapiens
human - (species)
Homo sapiens
human - (species) D
CCL3L1
Homo sapiens
human - (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
EARLY FLOWERING 3(ELF3)
Flowering time
Coding,
Indel
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Linkage Mapping
Jiménez-Gómez JM; Wallace AD; Maloof JN (2010)
Network analysis identifies ELF3 as a QTL for the shade avoidance response in Arabidopsis.
3 Additional References
GP00000244
ELF3
O82804
Physiology
Background-dependent effects of extensive polyQ coding variation
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
EARLY FLOWERING 3(ELF3)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
ERG11 = CYP51A1
Xenobiotic resistance
Coding,
Indel
Candida albicans
(species)
Intraspecific
Association Mapping
Coste A; Selmecki A; Forche A ; et al. (2007)
Genotypic evolution of azole resistance mechanisms in sequential Candida albicans isolates.
GP00000285
ERG11
P10613
Physiology
Copy number Variant
Candida albicans
(species)
Candida albicans
(species)
ERG11 = CYP51A1
Candida albicans
(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
Flavonoid 3'-hydroxylase (F3'H)
Coloration (flowers; pubescence; seeds)
Coding,
Indel
Glycine soja
(species)
Intraspecific
Candidate Gene
Guo Y; Qiu LJ (2013)
Allele-specific marker development and selection efficiencies for both flavonoid 3'-hydroxylase and [...]
GP00000317
CYP75B1
Q9SD85
Morphology
a single base insertion of an adenine at position 965 as well as a single base deletion of adenine at position 973 resulting in N322K and Q324T - exact causing mutation(s) unknown
Glycine max
soybean - (species)
Glycine soja
(species)
Flavonoid 3'-hydroxylase (F3'H)
Glycine soja
(species)
Published - Accepted by Curator
FLC (=Pep1)
Flowering time
Gene Amplification,
Indel
Arabis alpina
gray rockcress - (species)
Intraspecific
Candidate Gene
Albani MC; Castaings L; Wötzel S ; et al. (2012)
PEP1 of Arabis alpina is encoded by two overlapping genes that contribute to natural genetic variati[...]
GP00000329
FLC
Q9S7Q7
Physiology
complex structural variations
Arabis alpina
gray rockcress - (species)
Arabis alpina
gray rockcress - (species)
FLC (=Pep1)
Arabis alpina
gray rockcress - (species)
Published - Accepted by Curator
Frigida (FRI)
Flowering time
Coding,
Indel
N
Arabidopsis thaliana
thale cress - (species) D
Intraspecific
Linkage Mapping
Johanson U; West J; Lister C ; et al. (2000)
Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering tim[...]
1 Additional References
GP00000358
FRI
P0DH90
Physiology
376 bp deletion and 31 bp insertion that delete amino acid 1-15 and at best produce a 45-aa protein N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
Frigida (FRI)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
Frigida (FRI)
Flowering time
Coding,
Indel
N
Arabidopsis thaliana
thale cress - (species) D
Intraspecific
Candidate Gene
Le Corre V; Roux F; Reboud X (2002)
DNA polymorphism at the FRIGIDA gene in Arabidopsis thaliana: extensive nonsynonymous variation is c[...]
GP00000359
FRI
P0DH90
Physiology
Del 2257-2355 in exon 3; deletion of 99 bp combined with an insertion of 61 bp N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species) D
Frigida (FRI)
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
FUMARASE 2
Plant metabolism (fumarate/malate ratio)
Plant growth (bio-mass production)
Cis-regulatory,
Indel
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Linkage Mapping
Riewe D; Jeon HJ; Lisec J ; et al. (2016)
A naturally occurring promoter polymorphism of the Arabidopsis FUM2 gene causes expression variation[...]
1 Additional References
GP00001286
FUM2
Q9FI53
Physiology
Physiology
2068 bp in promotor region @position -395. AND 3833bp in promotor region @position -1107
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
FUMARASE 2
Arabidopsis thaliana
thale cress - (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
glb-5
CO2 avoidance
Aggregation behavior
Coding,
Indel
N
Caenorhabditis elegans
(species) D
Intraspecific
Linkage Mapping
McGrath PT; Rockman MV; Zimmer M ; et al. (2009)
Quantitative mapping of a digenic behavioral trait implicates globin variation in C. elegans sensory[...]
2 Additional References
GP00000399
glb-5
A3RMS5
Behavior
Behavior
765bp insertion/duplication resulting in a truncation of the last 179 amino acids of the protein and the inclusion of 40 different residues N
Caenorhabditis elegans
(species)
Caenorhabditis elegans
(species) D
glb-5
Caenorhabditis elegans
(species)
Published - Accepted by Curator
InR
Fertility
Developmental time
Body size
Stress response
Lifespan
Coding,
Indel
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Candidate Gene
Paaby AB; Bergland AO; Behrman EL ; et al. (2014)
A highly pleiotropic amino acid polymorphism in the Drosophila insulin receptor contributes to life-[...]
1 Additional References
GP00002663
InR
P09208
Morphology
Morphology; Physiology
Physiology
Physiology
Physiology
Deletion of 9 nucleotides in the first exon. The two alleles differ by presence/absence of the three amino acids QHH.
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
InR
Drosophila melanogaster
fruit fly - (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
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)
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
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
Period (per)
Locomotor activity (temperature sensitivity)
Coding,
Indel
Drosophila melanogaster
fruit fly - (species)
Intraspecific
Candidate Gene
Sawyer LA; Hennessy JM; Peixoto AA ; et al. (1997)
Natural variation in a Drosophila clock gene and temperature compensation.
GP00002002
per
P07663
Behavior
repeat (Thr-Gly) either 17 times or 20 times within the protein coding sequence
Drosophila melanogaster
fruit fly - (species)
Drosophila melanogaster
fruit fly - (species)
Period (per)
Drosophila melanogaster
fruit fly - (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
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
Pore-forming toxin-like (PFT)
Pathogen resistance (Fusarium)
Gene Loss,
Indel
N
Triticum aestivum
bread wheat - (species)
Intraspecific
Linkage Mapping
Rawat N; Pumphrey MO; Liu S ; et al. (2016)
Wheat Fhb1 encodes a chimeric lectin with agglutinin domains and a pore-forming toxin-like domain co[...]
GP00001563
Q4JEV5
Physiology
PFT gene is present and constitutively expressed in resistant line and absent in susceptible line N
Triticum aestivum
bread wheat - (species)
Triticum aestivum
bread wheat - (species)
Pore-forming toxin-like (PFT)
Triticum aestivum
bread wheat - (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
RPM1
Pathogen resistance
Gene Loss,
Indel
N
Arabidopsis thaliana
thale cress - (species)
Intraspecific
Linkage Mapping
Grant MR; McDowell JM; Sharpe AG ; et al. (1998)
Independent deletions of a pathogen-resistance gene in Brassica and Arabidopsis.
2 Additional References
GP00001000
RPM1
Q39214
Physiology
3.7kb indel with a null-state in the sensitive strains N
Arabidopsis thaliana
thale cress - (species)
Arabidopsis thaliana
thale cress - (species)
RPM1
Arabidopsis thaliana
thale cress - (species)
Published - Accepted by Curator
Rx1
Color vision (expression of SWS2b opsin)
Cis-regulatory,
Indel
Tramitichromis intermedius
(species)
Interspecific
Linkage Mapping
Schulte JE; O'Brien CS; Conte MA ; et al. (2014)
Interspecific variation in Rx1 expression controls opsin expression and causes visual system diversi[...]
GP00001441
rx1
O42356
Physiology
413bp deletion located 2.5-kb upstream of the Rx1 translation start site correlating with decreased Rx1 expression
Aulonocara baenschi
Nkhomo-benga peacock cichlid - (species)
Tramitichromis intermedius
(species)
Rx1
Tramitichromis intermedius
(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
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
Vacuolar transporter chaperone 1
Metal tolerance (copper)
Coding,
Indel
N
Saccharomyces cerevisiae
baker's yeast - (species) D
Experimental Evolution
Association Mapping
Gerstein AC; Ono J; Lo DS ; et al. (2015)
Too much of a good thing: the unique and repeated paths toward copper adaptation.
GP00001291
VTC1
P40046
Physiology
Pro > His+frameshift @ position 13 N
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species) D
Vacuolar transporter chaperone 1
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
Vacuolar transporter chaperone 4
Metal tolerance (copper)
Coding,
Indel
N
Saccharomyces cerevisiae
baker's yeast - (species) D
Experimental Evolution
Association Mapping
Gerstein AC; Ono J; Lo DS ; et al. (2015)
Too much of a good thing: the unique and repeated paths toward copper adaptation.
GP00001295
VTC4
P47075
Physiology
Phe > Ser+frameshift @ position 380 N
Saccharomyces cerevisiae
baker's yeast - (species)
Saccharomyces cerevisiae
baker's yeast - (species) D
Vacuolar transporter chaperone 4
Saccharomyces cerevisiae
baker's yeast - (species)
Published - Accepted by Curator
VRN1
Flowering time
Cis-regulatory,
Indel
Lolium perenne
(species)
Intraspecific
Candidate Gene
Asp T; Byrne S; Gundlach H ; et al. (2011)
Comparative sequence analysis of VRN1 alleles of Lolium perenne with the co-linear regions in barley[...]
GP00001183
VRN1
Q8L3W1
Physiology
8.6kb indel in first intron
Lolium perenne
(species)
Lolium perenne
(species)
VRN1
Lolium perenne
(species)
Published - Accepted by Curator
WntA
Coloration (wing, Mullerian mimicry)
Cis-regulatory,
Indel
Heliconius cydno
(species)
Intraspecific
Linkage Mapping
Gallant JR; Imhoff VE; Martin A ; et al. (2014)
Ancient homology underlies adaptive mimetic diversity across butterflies.
1 Additional References
GP00001209
WntA
A0A077DF90
Morphology
1.8-kb indel that was perfectly associated with variation in forewing melanin patterning
Heliconius cydno
(species)
Heliconius cydno
(species)
WntA
Heliconius cydno
(species)
Published - Accepted by Curator