Table 3 SNPs that met significance level of -log10(P) > 4 for the GWAS of canopy wilting
LocusaChr.bPos.cSNP-log10(P)MAFdEffecteEnvfSoyBase QTLg
114015639ss7155793245.130.27−1.62KS-16
2151961463ss7155801874.780.092.13ALL
323165348ss7155818235.340.06−3.65GA-15Canopy wilt 3-4, 3-8, 3-11, 6-1; mqCanopy wilt-001
4242073473ss7155828424.730.371.97GA-15Canopy wilt 6-3
5446096228ss7155882775.020.38−1.97GA-15
656207961ss7155922884.130.06−3.19GA-16Canopy wilt 3-5
7541387548ss7155917004.450.211.91GA-15
8613090474ss7155929917.050.062.97GA-16
9614258126ss7155931894.560.061.51KS-15
10647633030ss7155947386.750.28−1.87GA-16Canopy wilt 3-12
11649189084ss7155950125.940.371.50ALL
12711177483ss7155961714.400.320.71KS-15
1381699023ss7155998754.940.241.40ALL
1489837263ss7156029014.360.15−1.42ALL
15834471238ss7156014844.140.201.79KS-16
1691769730ss7156031684.530.18−1.93KS-16
17936942176ss7156036806.840.31−2.01GA-16
1810270252ss7156060546.630.471.81KS-16
19103598580ss7156063488.410.413.20GA-15
201023376136ss7156058048.260.27−3.31GA-16
211030831897ss7156061575.410.153.43GA-16
221131929823ss7156102505.250.48−1.45GA-16
23122053039ss7156117555.260.08−1.38KS-15
24122839426ss7156120024.820.35−1.43KS-16
251329459954ss7156148034.250.10−1.89GA-16
26143078346ss7156182735.130.431.55GA-16Canopy wilt 1-2
271410057919ss7156173664.150.072.76GA-16
281443597753ss7156189156.210.36−0.90KS-15
291512437556ss7156204425.490.341.29ALL
301550499617ss7156226477.590.242.16GA-16
311551622014ss7156228054.600.23−1.75GA-15
3216164715ss7156235385.490.481.81GA-15
16517535ss7156251925.040.09−1.29KS-15
33179384325ss7156283785.120.430.75KS-15Canopy wilt 1-3, 3-10, 3-13; mqCanopy wilt-006
341731794022ss7156267267.780.122.51ALLCanopy wilt 5-2
351736227875ss7156269687.640.093.47GA-16
361846860521ss7156311535.780.13−1.26KS-15
371854371258ss7156320375.310.091.47KS-15
3819809326ss7156362934.040.28−1.80GA-15
391938109922ss7156346887.730.15−2.16ALLCanopy wilt 2-7, 4-3
1938109922ss7156346886.980.15−3.05GA-15Canopy wilt 2-7, 4-3
401945307395ss7156354604.610.341.47GA-16Canopy wilt 5-4, 6-2
4120294010ss7156372185.170.461.55GA-16
422039013106ss7156379915.030.36−1.56GA-15
432046438247ss7156387484.300.46−1.71GA-15
442047435005ss7156389004.650.48−1.46ALL
  • a If multiple SNPs were identified in the same linkage disequilibrium (LD) block they were deemed part of the same locus (genomic region).

  • b Chromosome.

  • c Glyma.Wm82.a2 physical position.

  • d Minor allele frequency.

  • e Allelic effects were calculated by taking the difference in mean canopy wilting score between the two alleles at a particular SNP, and the direction, negative or positive, of the allelic effect estimates are relative to the alphabetical order of the nucleotides at each particular marker.

  • f Environment written as location-year-population.

  • g Canopy wilting QTL identified on SoyBase in which loci from our study are located within.