Table 3.
The genome-wide significant single nucleotide polymorphisms (SNPs) associated with production and immune-related traits.
| SNP information | SNP effect | Gene symbol within the SNP ± 200 kbp region | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Traitsa | SSC | Position (bp) | refSNP variation ID | EA | EAF | Βb | Proportionc | p-value | ||
| Production traits | ||||||||||
| BF | 1 | ######## | rs80975749 | A | 0.46 | −1.43 | (0.28) | 0.08 | 4.23E−07 | SERPINB13,SERPINB12,SERPINB5,VPS4B,KDSR |
| Immune-related traits | ||||||||||
| CAPA_105 | 3 | 2,64,34,892 | rs81229756 | A | 0.09 | −0.13 | (0.03) | 0.04 | 6.08E−07 | TMC5,TMC7,COQ7,ITPRIPL2,SYT17 |
| CAPA_105 | 3 | 2,64,39,289 | rs81312964 | A | 0.09 | −0.13 | (0.03) | 0.04 | 6.08E−07 | TMC5,TMC7,COQ7,ITPRIPL2,SYT17 |
| CAPA_105 | 3 | 2,70,30,167 | rs81379304 | A | 0.09 | −0.13 | (0.03) | 0.04 | 3.92E−07 | XYLT1 |
| RGL_105 | 7 | 1,82,10,546 | rs80902125 | G | 0.12 | −0.06 | (0.01) | 0.03 | 2.63E−07 | – |
| CORT_105 | 5 | 8,08,08,190 | rs81326027 | G | 0.48 | 0.10 | (0.02) | 0.04 | 1.67E−07 | NT5DC3 |
| CORT_105 | 7 | ######## | rs80996428 | A | 0.27 | 0.10 | (0.02) | 0.04 | 9.14E−07 | 192405031432500PRIMA1,ASB2,CCDC197,OTUB2 |
| CORT_105 | 7 | ######## | rs80918930 | C | 0.40 | 0.11 | (0.02) | 0.06 | 7.35E−11 | ISG12(A),PPP4R4,SERPINA6,SERPINA1,SERPINA11,UABP-2,SERPINA12 |
| CORT_105 | 7 | ######## | rs80966458 | G | 0.13 | 0.14 | (0.03) | 0.04 | 2.72E−07 | PPP4R4,SERPINA6,SERPINA1,SERPINA11,UABP-2,SERPINA12 |
| CORT_105 | 7 | ######## | rs80953170 | G | 0.29 | 0.10 | (0.02) | 0.04 | 2.74E−07 | PPP4R4,SERPINA6,SERPINA1,SERPINA11,UABP-2,SERPINA12,SERPINA4,SERPINA5 |
| CORT_7w | 10 | 6,34,10,258 | rs81236875 | A | 0.05 | 0.19 | (0.04) | 0.04 | 3.12E−07 | GATA3,TAF3,ATP5F1C,KIN |
SSC Sus scrofa chromosome, EA effect allele, EAF effect allele frequency.
aAbbreviations of traits are shown in Table 2.
bStandard errors are shown in parentheses.
cThe proportion of adjusted phenotypic variance explained by the SNP effects.