Table 3.
Significant SNPs and Indels of FarmCPU GWAS for ADIFF.
| SNP | SSC | Position | Effect | p-Value | QTLs * | Annotation | Gene (Distance from the Gene in bp) |
|---|---|---|---|---|---|---|---|
| rs325963999 # | 3 | 19301837 | 0.27 | 7.82 × 10−15 | 5224, 7455, 7472 | intronic | KATNIP(within) |
| rs693622708 | 6 | 39540583 | 0.17 | 8.58 × 10−9 | 24,289 | intergenic | UQCRFS1(166710), ENSSSCG00000050718(41760) |
| rs326134805 | 8 | 88543901 | 0.13 | 3.81 × 10−15 | 7477, 1100 | intergenic | ENSSSCG00000044017(86061),SLC7A11(63983) |
| rs1109963100 # | 10 | 2911179 | 0.33 | 3.74 × 10−13 | intergenic | ENSSSCG00000042899(210778),BRINP3(52348) | |
| rs1113875395 | 12 | 11463144 | 0.16 | 7.51 × 10−9 | 5227, 1128 | intergenic | ABCA8(15848),ENSSSCG00000045738(20026) |
| rs343773900 | 13 | 110154062 | 0.24 | 5.42 × 10−15 | 7479 | intronic | PLD1(within) |
| rs333970515 | 13 | 132158230 | −0.18 | 3.99 × 10−13 | 7479 | ncRNA_exonic | ENSSSCG00000047632(within) |
| rs1109225784 # | 15 | 12581324 | 0.32 | 1.46 × 10−16 | intergenic | U6(133156),U6(186459) | |
| rs322863105 # | 17 | 7610979 | −0.34 | 3.34 × 10−13 | intergenic | ENSSSCG00000045345(132678),ENSSSCG00000047202(438984) | |
| Indel | |||||||
| chr1:77875820 # | 1 | 77875820 | 0.17 | 1.02 × 10−7 | intergenic | FYN(65243),U6(107381) | |
| chr1:118273285 # | 1 | 118273285 | −0.35 | 1.74 × 10−10 | 5223, 6481, 5255 | intergenic | ENSSSCG00000049391(9019),ENSSSCG00000045826(5556) |
| rs788352632 | 2 | 62598411 | −0.12 | 3.81 × 10−10 | 909 | ncRNA_intronic | ENSSSCG00000048292(within) |
| chr11:6896071 | 11 | 6896071 | −0.13 | 1.22 × 10−8 | 5260 | ncRNA_intronic | ENSSSCG00000036846(within) |
| rs787621311 | 13 | 110898097 | 0.23 | 2.27 × 10−7 | 7479 | intronic | FNDC3B(within) |
| rs701717756 | 14 | 38222283 | 0.26 | 9.42 × 10−10 | intergenic | RBM19(17536),ENSSSCG00000042669(3247) | |
| chr14:91416556 | 14 | 91416556 | −0.30 | 1.34 × 10−9 | intergenic | ENSSSCG00000047278(204580),CXCL12(99865) | |
| chr15:84277014 # | 15 | 84277014 | 0.22 | 2.92 × 10−9 | 7468 | intergenic | ENSSSCG00000036052(46519),ENSSSCG00000038561(122000) |
| rs700363122 # | 17 | 8173767 | 0.40 | 9.10 × 10−16 | intergenic | ENSSSCG00000047202(116838),U6(28063) |
* QTL number in in PigQTL database. # Duplicate signals between GLM and FarmCPU. Effect means additive effect. ADIFF: the absolute difference between left and right teat number (ADIFF = |LTN − RTN|).