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Table 3 Significant SNPs associated with teat number in Canadian 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
1rs333890665271,354,4240.311.28E-050.8I4.861.42VPRRC2Bwithin
1rs321500205271,382,2730.451.40E-050.94I4.43–6.090.79–1.47II,III,IV,VENSSSCG0000002213036,815
2rs81363870121,140,4880.49   4.02–6.414.77–7.26II,III,IV,VSEMA6A453,157
3rs3446494665,715,2280.35   3.15–3.510.78–1.42II,IIINPTX2− 5452
5rs8138481366,721,3160.06   3.522.54IIPRMT8within
5rs8138483866,734,3880.1   3.921.52VPRMT8within
6rs324552394164,807,7450.24   3.580.77VEFCAB14within
7rs808647497,655,9110.36   3.240.79IIIELOVL2within
7rs3307836209,154,2930.15   3.180.37IVPHACTR1−191,156
7rs8088893696,128,6540.352.67E-073.78I   ENSSSCG00000033840122,929
7rs32461419496,278,6170.471.11E-146.07I   ENSSSCG00000028159−10,186
7rs33180720496,632,2170.361.46E-073.9I   NUMBwithin
7rs8126587596,660,8610.361.38E-073.92I   NUMBwithin
7rs32943424696,694,3640.369.91E-083.97I   NUMBwithin
7rs8139602996,727,4970.361.46E-073.9I   NUMBwithin
7rs8129528196,731,8380.352.25E-073.79I   NUMBwithin
7rs8139604096,743,5250.361.50E-073.9I   NUMBwithin
7rs8122758096,786,7140.352.47E-073.79I   NUMBwithin
7rs8139604396,806,7750.352.49E-073.77I   NUMB6800
7rs34268591997,048,5140.441.93E-135.84I   ENSSSCG00000035322−708
7rs8084383497,109,7720.351.63E-073.76I   ELMSAN132,738
7rs8080526497,126,5830.351.63E-073.76I   ENSSSCG00000002351−47,593
7rs32735781197,347,2820.334.97E-145.61I   BBOF1within
7rs31929625997,394,2960.331.76E-135.5I   LIN52within
7rs34628730997,427,8490.331.99E-135.48I   LIN52within
7rs69264084597,568,2840.487.51E-218.68I36.469.31VABCD4within
7rs111396099397,575,0680.487.54E-218.68I   ABCD4within
7rs33003212397,584,2870.487.54E-218.68I   ABCD4within
7VRTN_mutation97,615,8800.496.81E-207.8I   VRTNwithin
7rs34324894397,617,9070.487.54E-218.68I   VRTNwithin
7rs8089410697,652,6320.488.65E-208.34I   SYNDIG1L− 4101
7rs8123863997,946,6660.462.28E-095.23I   FCF1within
7rs8086470597,954,2580.462.29E-095.23I   FCF1within
7rs8092921597,973,8600.462.29E-095.23I   YLPM1− 2277
7rs8081347398,066,9110.474.67E-167.73I   PROX2within
7rs8083626798,089,2860.475.07E-167.71I   DLST− 1527
7rs80865802102,479,7250.335.99E-052.98I   ENSSSCG00000021315within
7rs338075156102,513,4430.333.84E-053.01I   ENSSSCG00000021315within
7rs80975884102,552,1050.333.84E-053.01I   ENSSSCG00000021315within
7rs80822795102,658,8220.303.96E-053.02I   ENSSSCG00000021315within
7rs80795811103,109,6780.195.27E-052.82I   DIO2within
7NA103,132,4350.195.27E-052.82I   DIO2within
7rs80847916103,151,3230.195.27E-052.82I   DIO2within
7NA103,164,9500.195.27E-052.82I   DIO2within
8rs8140128572,626,6380.33   5.750.9IVSEPT11within
8rs34348841573,599,0160.36   6.522.5IIFRAS1within
8rs81335362136,866,0260.16   3.281.1VBMP3−12,934
10rs33439254816,387,4850.47   4.030.97IISDCCAG8within
11rs808037906,291,0440.264.86E-061.11I3.12–5.390.51–2.39II,III,IV,VMTUS2within
11rs809146016,324,8340.276.52E-060.93I   MTUS2within
11rs34337711115,473,0250.36   3.291IIMRPS31801
11rs8093072370,370,3120.29   3.81–4.210.62–1.33III,IV,VFGF14within
12rs8144098317,695,2330.33   3.96–4.530.84–1.59II,IIIWNT3within
13rs335055280244,2350.11   3.97–5.351.60–3.59II,IIICPNE4−123,572
13rs345752157198,613,3090.2   3.42–3.660.86–1.58II,VRUNX1within
14rs34530724324,753,9920.39   4.070.91VPIWIL1within
14rs8145084057,407,4620.24   4.56–6.500.77–2.68II,III,IV,VENSSSCG00000010164−17,318
14rs80823799136,408,2160.18   3.310.78IIIDOCK1within
16rs3229850996,124,9520.312.53E-050.59I3.34–4.090.48–1.37II,III,IV,VMYO10within
17rs808436108,468,6540.44   3.00–5.390.36–1.25II,III,IV,VFAT1within
18rs3219427936,398,4310.26   3.94–4.241.38–1.99II,IIIGIMAP2within
18rs8147114451,455,2000.41   5.171.1IIHECW1within
  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