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Table 1 Peak SNP and benefical allele associated with resistance to the Hg Type 2.5.7 (race 1) identified by GWAS

From: Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7

SNP Chromosome Position -log10(p) MAF Model Resistant allele Susceptible alleles Average FI of accessions with resistant allele Average FI of accessions with susceptible allele Average FI of population
rs7631207 8 7,631,207 11.89 0.12 CMLM C G 22.71 111.07 104.19
rs7640250 8 7,640,250 11.89 0.12 CMLM C G 22.71 111.07 104.19
rs7671170 8 7,671,170 11.89 0.12 CMLM G C 22.71 111.07 104.19
rs7662003 8 7,662,003 10.51 0.12 CMLM T C 39.36 110.13 104.19
rs7664479 8 7,664,479 10.51 0.14 CMLM C A 39.02 109.75 104.19
rs7622492 8 7,622,492 10.2 0.11 CMLM A G 24.19 110.39 104.19
rs7661660 8 7,661,660 9.82 0.12 CMLM C A 39.36 109.97 104.19
rs46625879 18 46,625,879 7.12 0.1 CMLM G T 44.55 107.59 104.19
rs36423980 7 36,423,980 5.74 0.17 CMLM A G 49.27 112.53 104.19
rs3853672 14 3,853,672 5.53 0.1 CMLM A T 53.89 107.40 104.19
rs7631207 8 7,631,207 11.89 0.12 ECMLM C G 22.71 111.07 104.19
rs7640250 8 7,640,250 11.89 0.12 ECMLM C G 22.71 111.07 104.19
rs7671170 8 7,671,170 11.89 0.12 ECMLM G C 22.71 111.07 104.19
rs7662003 8 7,662,003 10.51 0.12 ECMLM T C 39.36 110.13 104.19
rs7664479 8 7,664,479 10.51 0.14 ECMLM C A 39.02 109.75 104.19
rs7622492 8 7,622,492 10.2 0.11 ECMLM A G 24.19 110.39 104.19
rs7661660 8 7,661,660 9.82 0.12 ECMLM C A 39.36 109.97 104.19
rs46625879 18 46,625,879 7.12 0.1 ECMLM G T 44.55 107.59 104.19
rs36423980 7 36,423,980 5.74 0.17 ECMLM A G 49.27 112.53 104.19
rs3853672 14 3,853,672 5.53 0.1 ECMLM A T 53.89 107.40 104.19
rs7671170 8 7,671,170 38.91 0.12 FARMCPU G C 22.71 111.07 104.19
rs46625879 18 46,625,879 23.93 0.1 FARMCPU G T 44.55 107.59 104.19
rs35898587 7 35,898,587 19.04 0.07 FARMCPU A C 48.30 107.38 104.19
rs16268025 8 16,268,025 11.48 0.06 FARMCPU A G 71.46 106.50 104.19
rs38522986 15 38,522,986 6.12 0.05 FARMCPU A G 52.14 107.16 104.19