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. 2018 May 31;31(12):1852–1862. doi: 10.5713/ajas.18.0072

Table 4.

The regions of 5 SNP windows which explained >1% of genetic variance for six reproduction traits in Large White, with a list of annotated genes

Traits SSC SNP position Reference SNP ID number Gene location1) (bp) Candidate gene1) %(var)2)
PWL 1 139481542 rs80830052 139,450,945–139,492,015 ALDH1A3 4.27
1 139579572 rs80930659 139,494,121–139,624,607 LRRK1 4.24
1 139608452 rs80804265 139,494,121–139,624,607 LRRK1 4.24
1 139636710 rs80862569 12.10 kb upstream gene LRRK1 4.24
1 139655026 rs80846651 30.41 kb upstream gene LRRK1 4.24
X 91880535 rs81473442 91,724,620–91,880,064 TRPC5 1.24
X 92070342 rs81323503 91,920,451–92,333,326 RTL4 1.65
X 92244402 rs81283192 91,920,451–92,333,326 RTL4 1.64
X 92330719 rs337547716 91,920,451–92,333,326 RTL4 1.61
X 92447181 rs80834138 92,418,941–92,486,688 LHFPL1 1.47
BAL 1 139481542 rs80830052 139,450,945–139,492,015 ALDH1A3 4.75
1 139579572 rs80930659 139,494,121–139,624,607 LRRK1 4.79
1 139608452 rs80804265 139,494,121–139,624,607 LRRK1 4.80
1 139636710 rs80862569 12.10 kb upstream gene LRRK1 4.83
1 139655026 rs80846651 30.41 kb upstream gene LRRK1 4.86
X 91880535 rs81473442 91,724,620–91,880,064 TRPC5 1.32
X 92070342 rs81323503 91,920,451–92,333,326 RTL4 1.76
X 92244402 rs81283192 91,920,451–92,333,326 RTL4 1.76
X 92330719 rs337547716 91,920,451–92,333,326 RTL4 1.76
X 92447181 rs80834138 92,418,941–92,486,688 LHFPL1 1.62
X 118854990 rs81339510 20.04 upstream gene SLITRK2 1.01
W2CL 1 139481542 rs80830052 139,450,945–139,492,015 ALDH1A3 3.52
1 139579572 rs80930659 139,494,121–139,624,607 LRRK1 3.65
1 139608452 rs80804265 139,494,121–139,624,607 LRRK1 3.65
1 139636710 rs80862569 12.10 kb upstream gene LRRK1 3.66
1 139655026 rs80846651 30.41 kb upstream gene LRRK1 3.66
X 113854897 rs80912014 113,460,191–113,955,691 FGF13 0.99
X 113870858 rs80968752 113,460,191–113,955,691 FGF13 0.99
X 113889934 rs80865791 113,460,191–113,955,691 FGF13 0.99
X 113913461 rs80827323 113,460,191–113,955,691 FGF13 0.99
X 118839264 rs328629988 4.31 upstream gene SLITRK2 2.72
X 118854990 rs81339510 20.04 upstream gene SLITRK2 2.99
LSY 1 139481542 rs80830052 139,450,945–139,492,015 ALDH1A3 1.32
1 139579572 rs80930659 139,494,121–139,624,607 LRRK1 1.37
1 139608452 rs80804265 139,494,121–139,624,607 LRRK1 1.39
1 139655026 rs80846651 30.41 kb upstream gene LRRK1 1.45
1 139636710 rs80862569 12.10 kb upstream gene LRRK1 1.43
LSY 18 7404576 rs81467652 7,346,793–7,419,859 EPHB6 1.00
X 91880535 rs81473442 91,724,620–91,880,064 TRPC5 1.27
X 92070342 rs81323503 91,920,451–92,333,326 RTL4 1.64
X 92244402 rs81283192 91,920,451–92,333,326 RTL4 1.62
X 92330719 rs337547716 91,920,451–92,333,326 RTL4 1.59
X 92447181 rs80834138 92,418,941–92,486,688 LHFPL1 1.45
PWSY 1 139481542 rs80830052 139,450,945–139,492,015 ALDH1A3 1.30
1 139579572 rs80930659 139,494,121–139,624,607 LRRK1 1.27
1 139608452 rs80804265 139,494,121–139,624,607 LRRK1 1.26
1 139636710 rs80862569 12.10 kb upstream gene LRRK1 1.25
1 139655026 rs80846651 30.41 kb upstream gene LRRK1 1.24
X 91880535 rs81473442 91,724,620–91,880,064 TRPC5 1.43
X 92070342 rs81323503 91,920,451–92,333,326 RTL4 1.86
X 92244402 rs81283192 91,920,451–92,333,326 RTL4 1.85
X 92330719 rs337547716 91,920,451–92,333,326 RTL4 1.82
X 92447181 rs80834138 92,418,941–92,486,688 LHFPL1 1.67
NPD 1 139481542 rs80830052 139,450,945–139,492,015 ALDH1A3 1.24
1 139579572 rs80930659 139,494,121–139,624,607 LRRK1 1.29
1 139608452 rs80804265 139,494,121–139,624,607 LRRK1 1.30
1 139655026 rs80846651 30.41 kb upstream gene LRRK1 1.36
1 139636710 rs80862569 12.10 kb upstream gene LRRK1 1.34
18 7404576 rs81467652 7,346,793–7,419,859 EPHB6 1.10
X 7310670 rs81473166 7,237,938–7,421,430 MID1 1.06
X 7483667 rs80838369 7,235,386–7,906,049 MID1 1.04
X 7576417 rs81473214 7,235,386–7,906,049 MID1 1.05
X 7702300 rs81473219 7,235,386–7,906,049 MID1 1.05
X 91880535 rs81473442 91,724,620–91,880,064 TRPC5 1.15
X 92070342 rs81323503 91,920,451–92,333,326 RTL4 1.44
X 92244402 rs81283192 91,920,451–92,333,326 RTL4 1.43
X 92330719 rs337547716 91,920,451–92,333,326 RTL4 1.40
X 92447181 rs80834138 92,418,941–92,486,688 LHFPL1 1.30
X 118275204 rs81473813 173.66 kb downstream Uncharacterized 1.57

SNP, single nucleotide polymorphism; SSC, the position of SNP on Sus scrofa chromosome; PWL, pigs weaned per litters; ALDH1A3, aldehyde dehydrogenase 1 family member A3; LRRK1, leucine rich repeat kinase 1; TRPC5, transient receptor potential cation channel subfamily C member 5; RTL4, retrotransposon Gag like 4; LHFPL1, LHFPL tetraspan subfamily member 1; BAL, born alive per litters; SLITRK2, SLIT and NTRK like family member 2; W2CL, wean to conception interval per litters; FGF13, fibroblast growth factor 13; LSY, litter per sow per year; EPHB6, EPH receptor B6; PWSY, pig weaned per sow per year; NPD, non-productive day; MID1, midline-1.

1)

Gene locations on the Sus scrofa Build 11.1 assembly and the upstream and downstream of regions that possibly associated with each reproduction traits. Gene names represent on Ensembl (http://asia.ensembl.org/Sus_scrofa/Info/Index).

2)

Percentage of genetic variance explained by windows of 5 adjacent SNPs.