Table 3.
Significant SNPs associated with teat number in Canadian Duroc pigs
| SSCa | SNP ID | Position (bp)b | MAF | Single-locus GWAS | Multi-locus GWAS | Nearest genee | Distance/bpf | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| P-value | R2(%)c | Modeld | LOD | R2(%)c | Modeld | ||||||
| 1 | rs333890665 | 271,354,424 | 0.31 | 1.28E-05 | 0.8 | I | 4.86 | 1.42 | V | PRRC2B | within |
| 1 | rs321500205 | 271,382,273 | 0.45 | 1.40E-05 | 0.94 | I | 4.43–6.09 | 0.79–1.47 | II,III,IV,V | ENSSSCG00000022130 | 36,815 |
| 2 | rs81363870 | 121,140,488 | 0.49 | 4.02–6.41 | 4.77–7.26 | II,III,IV,V | SEMA6A | 453,157 | |||
| 3 | rs344649466 | 5,715,228 | 0.35 | 3.15–3.51 | 0.78–1.42 | II,III | NPTX2 | − 5452 | |||
| 5 | rs81384813 | 66,721,316 | 0.06 | 3.52 | 2.54 | II | PRMT8 | within | |||
| 5 | rs81384838 | 66,734,388 | 0.1 | 3.92 | 1.52 | V | PRMT8 | within | |||
| 6 | rs324552394 | 164,807,745 | 0.24 | 3.58 | 0.77 | V | EFCAB14 | within | |||
| 7 | rs80864749 | 7,655,911 | 0.36 | 3.24 | 0.79 | III | ELOVL2 | within | |||
| 7 | rs330783620 | 9,154,293 | 0.15 | 3.18 | 0.37 | IV | PHACTR1 | −191,156 | |||
| 7 | rs80888936 | 96,128,654 | 0.35 | 2.67E-07 | 3.78 | I | ENSSSCG00000033840 | 122,929 | |||
| 7 | rs324614194 | 96,278,617 | 0.47 | 1.11E-14 | 6.07 | I | ENSSSCG00000028159 | −10,186 | |||
| 7 | rs331807204 | 96,632,217 | 0.36 | 1.46E-07 | 3.9 | I | NUMB | within | |||
| 7 | rs81265875 | 96,660,861 | 0.36 | 1.38E-07 | 3.92 | I | NUMB | within | |||
| 7 | rs329434246 | 96,694,364 | 0.36 | 9.91E-08 | 3.97 | I | NUMB | within | |||
| 7 | rs81396029 | 96,727,497 | 0.36 | 1.46E-07 | 3.9 | I | NUMB | within | |||
| 7 | rs81295281 | 96,731,838 | 0.35 | 2.25E-07 | 3.79 | I | NUMB | within | |||
| 7 | rs81396040 | 96,743,525 | 0.36 | 1.50E-07 | 3.9 | I | NUMB | within | |||
| 7 | rs81227580 | 96,786,714 | 0.35 | 2.47E-07 | 3.79 | I | NUMB | within | |||
| 7 | rs81396043 | 96,806,775 | 0.35 | 2.49E-07 | 3.77 | I | NUMB | 6800 | |||
| 7 | rs342685919 | 97,048,514 | 0.44 | 1.93E-13 | 5.84 | I | ENSSSCG00000035322 | −708 | |||
| 7 | rs80843834 | 97,109,772 | 0.35 | 1.63E-07 | 3.76 | I | ELMSAN1 | 32,738 | |||
| 7 | rs80805264 | 97,126,583 | 0.35 | 1.63E-07 | 3.76 | I | ENSSSCG00000002351 | −47,593 | |||
| 7 | rs327357811 | 97,347,282 | 0.33 | 4.97E-14 | 5.61 | I | BBOF1 | within | |||
| 7 | rs319296259 | 97,394,296 | 0.33 | 1.76E-13 | 5.5 | I | LIN52 | within | |||
| 7 | rs346287309 | 97,427,849 | 0.33 | 1.99E-13 | 5.48 | I | LIN52 | within | |||
| 7 | rs692640845 | 97,568,284 | 0.48 | 7.51E-21 | 8.68 | I | 36.46 | 9.31 | V | ABCD4 | within |
| 7 | rs1113960993 | 97,575,068 | 0.48 | 7.54E-21 | 8.68 | I | ABCD4 | within | |||
| 7 | rs330032123 | 97,584,287 | 0.48 | 7.54E-21 | 8.68 | I | ABCD4 | within | |||
| 7 | VRTN_mutation | 97,615,880 | 0.49 | 6.81E-20 | 7.8 | I | VRTN | within | |||
| 7 | rs343248943 | 97,617,907 | 0.48 | 7.54E-21 | 8.68 | I | VRTN | within | |||
| 7 | rs80894106 | 97,652,632 | 0.48 | 8.65E-20 | 8.34 | I | SYNDIG1L | − 4101 | |||
| 7 | rs81238639 | 97,946,666 | 0.46 | 2.28E-09 | 5.23 | I | FCF1 | within | |||
| 7 | rs80864705 | 97,954,258 | 0.46 | 2.29E-09 | 5.23 | I | FCF1 | within | |||
| 7 | rs80929215 | 97,973,860 | 0.46 | 2.29E-09 | 5.23 | I | YLPM1 | − 2277 | |||
| 7 | rs80813473 | 98,066,911 | 0.47 | 4.67E-16 | 7.73 | I | PROX2 | within | |||
| 7 | rs80836267 | 98,089,286 | 0.47 | 5.07E-16 | 7.71 | I | DLST | − 1527 | |||
| 7 | rs80865802 | 102,479,725 | 0.33 | 5.99E-05 | 2.98 | I | ENSSSCG00000021315 | within | |||
| 7 | rs338075156 | 102,513,443 | 0.33 | 3.84E-05 | 3.01 | I | ENSSSCG00000021315 | within | |||
| 7 | rs80975884 | 102,552,105 | 0.33 | 3.84E-05 | 3.01 | I | ENSSSCG00000021315 | within | |||
| 7 | rs80822795 | 102,658,822 | 0.30 | 3.96E-05 | 3.02 | I | ENSSSCG00000021315 | within | |||
| 7 | rs80795811 | 103,109,678 | 0.19 | 5.27E-05 | 2.82 | I | DIO2 | within | |||
| 7 | NA | 103,132,435 | 0.19 | 5.27E-05 | 2.82 | I | DIO2 | within | |||
| 7 | rs80847916 | 103,151,323 | 0.19 | 5.27E-05 | 2.82 | I | DIO2 | within | |||
| 7 | NA | 103,164,950 | 0.19 | 5.27E-05 | 2.82 | I | DIO2 | within | |||
| 8 | rs81401285 | 72,626,638 | 0.33 | 5.75 | 0.9 | IV | SEPT11 | within | |||
| 8 | rs343488415 | 73,599,016 | 0.36 | 6.52 | 2.5 | II | FRAS1 | within | |||
| 8 | rs81335362 | 136,866,026 | 0.16 | 3.28 | 1.1 | V | BMP3 | −12,934 | |||
| 10 | rs334392548 | 16,387,485 | 0.47 | 4.03 | 0.97 | II | SDCCAG8 | within | |||
| 11 | rs80803790 | 6,291,044 | 0.26 | 4.86E-06 | 1.11 | I | 3.12–5.39 | 0.51–2.39 | II,III,IV,V | MTUS2 | within |
| 11 | rs80914601 | 6,324,834 | 0.27 | 6.52E-06 | 0.93 | I | MTUS2 | within | |||
| 11 | rs343377111 | 15,473,025 | 0.36 | 3.29 | 1 | II | MRPS31 | 801 | |||
| 11 | rs80930723 | 70,370,312 | 0.29 | 3.81–4.21 | 0.62–1.33 | III,IV,V | FGF14 | within | |||
| 12 | rs81440983 | 17,695,233 | 0.33 | 3.96–4.53 | 0.84–1.59 | II,III | WNT3 | within | |||
| 13 | rs335055280 | 244,235 | 0.11 | 3.97–5.35 | 1.60–3.59 | II,III | CPNE4 | −123,572 | |||
| 13 | rs345752157 | 198,613,309 | 0.2 | 3.42–3.66 | 0.86–1.58 | II,V | RUNX1 | within | |||
| 14 | rs345307243 | 24,753,992 | 0.39 | 4.07 | 0.91 | V | PIWIL1 | within | |||
| 14 | rs81450840 | 57,407,462 | 0.24 | 4.56–6.50 | 0.77–2.68 | II,III,IV,V | ENSSSCG00000010164 | −17,318 | |||
| 14 | rs80823799 | 136,408,216 | 0.18 | 3.31 | 0.78 | III | DOCK1 | within | |||
| 16 | rs322985099 | 6,124,952 | 0.31 | 2.53E-05 | 0.59 | I | 3.34–4.09 | 0.48–1.37 | II,III,IV,V | MYO10 | within |
| 17 | rs80843610 | 8,468,654 | 0.44 | 3.00–5.39 | 0.36–1.25 | II,III,IV,V | FAT1 | within | |||
| 18 | rs321942793 | 6,398,431 | 0.26 | 3.94–4.24 | 1.38–1.99 | II,III | GIMAP2 | within | |||
| 18 | rs81471144 | 51,455,200 | 0.41 | 5.17 | 1.1 | II | HECW1 | within | |||
aSus scrofa chromosome b SNP position in Ensembl c Proportion of total phenotypic variation explained by each SNP. Bold text indicates the maximum phenotypic variance explained by the multi-locus model d MLM, mrMLM, FASTmrMLM, FASTmrEMMA and ISIS EM-BLASSO were indicated by I-V, respectively. The bold data represent the model that explained largest phenotypic variance e Underline indicates that the gene was newly identified as a candidate for teat number f The SNP located upstream/downstream of the nearest gene