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Table 2 Significant SNPs associated with teat number in American Duroc pigs

From: Genome-wide association analyses identify known and novel loci for teat number in Duroc pigs using single-locus and multi-locus models

SSCaSNP IDPosition (bp)bMAFSingle-locus GWASMulti-locus GWASNearest geneeDistance/bpf
P-valueR2(%)cModeldLODR2(%)cModeld
1rs8129676626,423,6440.41   3.23–4.110.22–0.36II,III,VTNFAIP3−50,291
1rs8135336732,198,0140.024.83E-051.94I   AKAP7−23,051
1rs8135401449,632,5600.41   4.660.51IVADGRB312,781
1rs8080864550,037,5860.3   4.11.01VLMBRD159,597
1rs80855587166,253,3060.32   3.180.53VITGA11within
1rs80805477248,169,5560.46   3.12–5.680.41–0.68IV,VZNF462within
1rs81315010251,816,7900.14   41.39IIIENSSSCG00000005457within
2rs8135657927,110,3250.5   4.54–5.080.56–0.57II,III,VFBXO3−35,449
2rs33033301677,481,5980.11   4.150.48IVR3HDM4within
2rs338630193127,747,7670.19   3.60.73IIIZNF608−300,480
3rs8131440820,394,8930.11   3.28–4.120.80–1.32II,III,VENSSSCG00000039406−150,340
3rs8133801432,426,2870.05   4.822.78IIEMP2−24,223
4rs318980859117,518,6570.42   3.470.32IVVCAM17446
5rs34149116710,879,8980.35   4.38–4.770.36–0.55II,III,VNCF4within
5rs32859907975,707,7070.05   3.861.36VNELL2within
6rs8139540735,040,9920.27   3.12–3.430.55–0.80II,III,VZNF423within
6rs33359232849,265,8690.27   3.140.48IIIAXLwithin
6rs8138963289,786,9160.05   3.192.55VCSMD2within
6rs81391820134,798,2340.191.87E-051.28I5.19–7.160.62–3.03II,III,IV,VPTGFR21,471
6rs705289935168,268,2780.431.74E-050.38I3.010.29VENSSSCG00000039458−13,851
7rs8096437192,809,2310.49   4.080.49VDCAF5within
9rs8142022714,459,4520.44   3.090.17VENSSSCG00000014896−370,357
11rs8130543725,782,6580.15   3.43–4.820.94–1.45II,III,VENSSSCG00000036698within
11rs8080945134,924,1230.04   4.29–5.254.23–4.69II,IIIENSSSCG00000040542− 248,706
14rs34530724324,753,9920.47   4.570.5IVPIWIL1within
14rs8084816226,467,3690.49   3.210.27VTMEM132Cwithin
14rs8089076269,437,5180.21   3.030.29IVCTNNA3within
14rs321772507115,176,4550.018.3E-051.11I   CFAP432412
14rs327004523133,536,1150.38   3.641.07IICHST15within
14rs80794466137,506,3430.28   40.73VENSSSCG00000026302210,031
15rs80957887111,327,8960.5   3.720.41VENSSSCG00000023264within
15rs333698977129,904,5300.27   3.58–4.000.33–0.96IV,VPID1− 174,602
16rs8131666027,084,0560.38   3.77–6.240.38–1.90II,III,IV,VGHR−42,296
16rs8146190469,106,0540.48   3.220.39VMFAP3within
17rs31913465544,791,9740.31   3.490.44VENSSSCG00000038990within
  1. 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