Table 3.
The results of meta-analysis for total number of piglets born and number of piglets born alive traits across populations
| SNP name | SSC | Location (bp) | p(meta-TNB)–value1) | p(meta-NBA)–value2) | Associated gene3) | Distance4) (bp) | Gene function |
|---|---|---|---|---|---|---|---|
| ALGA0012964 | 2 | 32,799,355 | 9.23E-05 | 6.41E-09 | LIN7C | In | Morphogenesis of an epithelial sheet |
| ALGA0054421 | 9 | 104,625,702 | 1.17E-08 | 1.29E-05 | LHFPL3 | In | Self reported educational attainment |
| ASGA0037579 | 8 | 5,703,865 | 0.000156302 | 9.82E-07 | MSX1 | Down | In utero embryonic development |
| ASGA0082366 | 9 | 47,037,744 | 9.84E-07 | 0.000189917 | NECTIN1 | Down | Lens morphogenesis in camera-type eye |
| ALGA0113046 | 2 | 12,842,137 | 2.29E-07 | 0.000193931 | OR10Q1 | Up | G protein-coupled receptor signaling pathway |
| ASGA0104976 | 12 | 116,492,539 | 2.44E-08 | 0.000203328 | NA | ||
| DRGA0000439 | 1 | 30,456,989 | 2.86E-08 | 2.37E-05 | EYA4 | In | Protein dephosphorylation |
| H3GA0042513 | 14 | 126,349,106 | 0.000299386 | 2.80E-07 | GFRA1 | In | Nervous system development |
| WU_10.2_7_130172562 | 7 | 537,474 | 2.88E-05 | 3.27E-07 | FOXQ1 | Up | Cell differentiation |
| H3GA0021245 | 7 | 38,823,945 | 3.95E-08 | 3.11E-05 | VEGFA | Down | Regulation of signaling receptor activity |
| MARC0022141 | 1 | 0 | 4.11E-08 | 0.000318796 | NA | NA | NA |
| WU_10.2_4_80076056 | 4 | 73,428,123 | 0.00116 | 2.62E-07 | CA8 | Down | Phosphatidylinositol-mediated signaling |
| WU_10.2_1_11153176 | 1 | 9,032,844 | 3.51E-07 | 0.001559 | SYNJ2 | In | Inositol phosphate dephosphorylation |
| WU_10.2_3_129122235 | 3 | 120,870,358 | 7.72E-07 | 0.060399 | FAM49A | Up | NA |
| MARC0081527 | 6 | 80,617,330 | 0.000432722 | 3.20E-07 | C1QB | Down | Complement activation, classical pathway |
| WU_10.2_14_389214 | 14 | 217,583 | 5.23 E-08 | 8.22E-06 | SPIN1 | Up | Wnt signaling pathway |
| WU_10.2_2_12776809 | 2 | 13,143,791 | 0.000571848 | 3.33E-07 | CTNND1 | Up | Negative regulation of canonical Wnt signaling pathway |
| WU_10.2_6_85867859 | 6 | 92,797,244 | 6.21E-07 | 0.000352248 | GRIK3 | Up | Glutamate receptor signaling pathway |
| ALGA0012962 | 2 | 32,757,436 | 0.00064956 | 4.23E-07 | LIN7C | In | Morphogenesis of an epithelial sheet |
SNP, single nucleotide polymorphism; SSC, Sus scrofa chromosome; TNB, total number of piglets born; NBA, number of piglets born alive; LIN7C, lin-7 homolog C; LHFPL3, LHFPL tetraspan submily member 3; MSX1, msh homeobox 1; NECTIN1, nectin cell adhesion molecule 1; OR10Q1, olfactory receptor family 10 subfamily Q member 1; EYA4, EYA transcriptional coactivator and phosphatase 4; GFRA1, GDNF family receptor alpha 1; FOXQ1, forkhead box Q1; VEGFA, vascular endothelial growth factor A; CA8, carbonic anhydrase 8; SYNJ2, synaptojanin 2; FAM49A, family with sequence similarity 49 member A; C1QB, complement C1q B chain; SPIN1, spindlin 1; CTNND1, catenin delta 1; GRIK3, glutamate ionotropic receptor kainate type subunit 3; VA, not available.
p(meta-TNB)–value = p-value from the meta analysis. The bold data in this column represent the significant SNP at genome-wide significant level; otherwise at the chromosome-wide significant level.
p(meta-NBA)–value = p-value from the meta analysis. The bold data in this column represent the 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.