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
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
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
CHRNA1
Xenobiotic resistance (snake venom)
2 Mutations:
Coding
SNP
Sus scrofa
pig - (species) D
Intergeneric or Higher
Candidate Gene
Drabeck DH; Dean AM; Jansa SA (2015)
Why the honey badger don't care: Convergent evolution of venom-targeted nicotinic acetylcholine rece[...]
GP00001721
CHRNA1
P02708
Physiology
2 mutations
Carnivora
carnivores - (order)
Sus scrofa
pig - (species) D
CHRNA1
Sus scrofa
pig - (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
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
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
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
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,
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)
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
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,
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
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
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
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
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
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
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
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
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