Table 2.
The result of single population analysis for total number of piglets born and number of piglets born alive traits across populations
| SSC | SNP name | Location (bp) | Populations1) | p(NBA)-value2) | p(TNB)-value3) | Associated gene4) | Distance5) (bp) | Gene function |
|---|---|---|---|---|---|---|---|---|
| 17 | ALGA0094112 | 27,884,015 | XD | 1.160E-05 | 3.770E-05 | RIN2 | In | Signal transduction |
| 1 | WU_10.2_1_11153176 | 9,032,844 | XD | 1.686E-05 | 3.314E-05 | SYNJ2 | In | Inositol phosphate dephosphorylation |
| 6 | MARC0081527 | 80,617,330 | XD | 1.859E-05 | 1.780E-05 | C1QB | Down | Complement activation, classical pathway |
| 4 | WU_10.2_4_80076056 | 73,428,123 | XD | 2.188E-05 | 1.336E-05 | CA8 | Down | Phosphatidylinositol-mediated signaling |
| 2 | ALGA0113046 | 12,842,137 | XD | 2.132E-05 | 1.346E-05 | OR10Q1 | Up | G protein-coupled receptor signaling pathway |
| 5 | H3GA0015463 | 9,863,427 | XD | 3.220E-05 | 1.760E-05 | PICK1 | In | Intracellular protein transport |
| 4 | WU_10.2_4_80076056 | 73,428,123 | FJ | 1.807E-05 | 2.313E-05 | CA8 | Down | Phosphatidylinositol-mediated signaling |
| 12 | WU_10.2_12_17971455 | 41,032 | ZX | 1.080E-05 | 7.546E-04 | ZNF750 | Down | |
| 7 | WU_10.2_7_130172562 | 537,474 | ZX | 1.675E-05 | 1.040E-05 | FOXQ1 | Up | Cell differentiation |
| 1 | WU_10.2_1_11153176 | 9,032,844 | ZX | 6.517E-05 | 1.110E-05 | SYNJ2 | In | Inositol phosphate dephosphorylation |
| 7 | H3GA0021245 | 38,823,945 | ZX | 2.478E-05 | 1.125E-05 | VEGFA | Down | Regulation of signaling receptor activity |
| 1 | MARC0022141 | 0 | ZX | 1.172E-04 | 1.644E-05 | NA | NA | NA |
| 1 | DRGA0000439 | 30,456,989 | ZX | 1.918E-04 | 1.674E-05 | EYA4 | In | Protein dephosphorylation |
SSC, Sus scrofa chromosome; SNP, single nucleotide polymorphism; NBA, number of piglets born alive; TNB, total number of piglets born; RIN2, Ras and Rab interactor 2; SYNJ2, synaptojanin 2; C1QB, complement C1q B chain; CA, carbonic anhydrase 8; OR10Q1, olfactory receptor family 10 subfamily Q member 1; PICK1, protein interacting with PRKCA 1; ZNF750, zinc finger protein 750; FOXQ1, forkhead box Q1; VEGFA, vascular endothelial growth factor A; EYA4, EYA transcriptional coactivator and phosphatase 4; NA, not available; GWAS, genome-wide association study.
The results of significant SNPs from different populations.
p(NBA)–value = p-value from sing population GWAS for NBA.
p(TNB)–value = p-value from sing population GWAS for TNB. The bold data in this column represent the SNP at suggestive genome-wide significant level.
The associated gene in bold in this column represent these genes were associated with traits based on annotation.
down/up = the location of SNP in downstream/upstream of the nearest gene.