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

Table 3.

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

Traits SSC SNP position Reference SNP ID number Gene location1) (bp) Candidate gene1) % (var)2)
PWL 2 20563683 rs81291755 20,417,294 – 21,634,205 LRRC4C 1.04
2 20637563 rs81355894 20,417,294 – 21,634,205 LRRC4C 1.04
2 20665892 rs81355903 20,417,294 – 21,634,205 LRRC4C 1.04
2 20717076 rs81355915 20,417,294 – 21,634,205 LRRC4C 1.04
6 70313133 rs81320475 70,313,309–70,326,455 RBP7 3.36
6 70323076 rs81285644 70,313,309–70,326,455 RBP7 3.36
6 70408106 rs81275494 70,345,801–70,462,430 UBE4B 3.36
6 70418172 rs81279050 70,345,801–70,462,430 UBE4B 3.36
6 70428427 rs81270030 70,345,801–70,462,430 UBE4B 3.36
14 8994023 rs80863686 8,990,750–8,997,300 NEFL 1.04
14 9071879 rs80807276 74.57 kb upstream gene NEFL 1.04
BAL 2 20563683 rs81291755 20,417,294 – 21,634,205 LRRC4C 1.56
2 20637563 rs81355894 20,417,294 – 21,634,205 LRRC4C 1.56
2 20665892 rs81355903 20,417,294 – 21,634,205 LRRC4C 1.56
2 20717076 rs81355915 20,417,294 – 21,634,205 LRRC4C 1.56
2 125660328 rs81265647 3.09 kb upstream gene ZNF474 1.06
6 70313133 rs81320475 70,313,309–70,326,455 RBP7 3.06
6 70323076 rs81285644 70,313,309–70,326,455 RBP7 3.06
6 70408106 rs81275494 70,345,801–70,462,430 UBE4B 3.06
6 70418172 rs81279050 70,345,801–70,462,430 UBE4B 3.06
6 70428427 rs81270030 70,345,801–70,462,430 UBE4B 3.06
6 168897980 rs81345088 168,876,871–168,902,812 ZMYND12 1.08
6 168899114 rs81259198 168,876,871–168,902,812 ZMYND12 1.08
6 168916590 rs81245903 3.17 kb downstream gene RIMKLA 1.08
6 168931165 rs81273774 168,919,762–168,950,094 RIMKLA 1.08
W2CL 2 107889586 rs81362373 2.18 kb upstream gene SLCO4C1 1.11
2 107984868 rs81362382 107,922,002–108,020,311 SLCO6A1 1.09
2 108025814 rs81362385 5.50 kb upstream gene SLCO6A1 1.09
2 108070963 rs81245337 50.65 kb upstream gene SLCO6A1 1.23
6 70313133 rs81320475 70,313,309–70,326,455 RBP7 5.69
6 70323076 rs81285644 70,313,309–70,326,455 RBP7 5.69
6 70408106 rs81275494 70,345,801–70,462,430 UBE4B 5.69
6 70418172 rs81279050 70,345,801–70,462,430 UBE4B 5.69
6 70428427 rs81270030 70,345,801–70,462,430 UBE4B 5.69
X 7098283 rs80897515 80.54 kb upstream gene CLCN4 1.57
X 7106161 rs324666200 88.42 kb upstream gene CLCN4 1.42
X 7116982 rs80818513 99.24 kb upstream gene CLCN4 1.42
W2CL X 7213512 rs80991855 24.42 downstream gene MID1 1.42
LSY 2 107889586 rs81362373 2.18 kb upstream gene SLCO4C1 1.30
2 107984868 rs81362382 107,922,002–108,020,311 SLCO6A1 1.31
2 108025814 rs81362385 5.50 kb upstream gene SLCO6A1 1.32
2 108055321 rs81267184 35.01 kb upstream gene SLCO6A1 1.34
2 108070963 rs81245337 50.65 kb upstream gene SLCO6A1 2.05
X 7106161 rs324666200 88.42 kb upstream gene CLCN4 1.38
X 7116982 rs80818513 99.24 kb upstream gene CLCN4 1.38
X 7213512 rs80991855 24.42 downstream gene MID1 1.38
PWSY 2 108070963 rs81245337 50.65 kb upstream gene SLCO6A1 1.26
6 70313133 rs81320475 70,313,309–70,326,455 RBP7 1.67
6 70323076 rs81285644 70,313,309–70,326,455 RBP7 1.67
6 70408106 rs81275494 70,345,801–70,462,430 UBE4B 1.67
6 70418172 rs81279050 70,345,801–70,462,430 UBE4B 1.67
6 70428427 rs81270030 70,345,801–70,462,430 UBE4B 1.67
NPD 2 107889586 rs81362373 2.18 kb upstream gene SLCO4C1 1.39
2 107984868 rs81362382 107,922,002–108,020,311 SLCO6A1 1.41
2 108025814 rs81362385 5.50 kb upstream gene SLCO6A1 1.42
2 108055321 rs81267184 35.01 kb upstream gene SLCO6A1 1.44
2 108070963 rs81245337 50.65 kb upstream gene SLCO6A1 2.20
X 7213512 rs80991855 24.42 downstream gene MID1 1.37
X 7116982 rs80818513 99.24 kb upstream gene CLCN4 1.37
X 7106161 rs324666200 88.42 kb upstream gene CLCN4 1.37

SNP, single nucleotide polymorphism; SSC, the position of SNP on Sus scrofa chromosome; PWL, pigs weaned per litters; LRRC4C, leucine rich repeat containing 4C; RBP7, retinol binding protein 7; UBE4B, ubiquitination factor E4B; NEFL, neurofilament light; BAL, born alive per litters; ZNF474, zinc finger protein 474; ZMYND12, zinc finger MYND-type containing 12; RIMKLA, ribosomal modification protein rimK like family member A; W2CL, wean to conception interval per litters; MID1, midline-1; LSY, litter per sow per year; SLCO4C1, solute carrier organic anion transporter family member 4C1; CLCN4, chloride voltage-gated channel 4; PWSY, pig weaned per sow per year; NPD, non-productive day.

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.