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. 2019 Jan 1;6:9. doi: 10.1038/s41438-018-0085-3

Table 2.

Single nucleotide polymorphisms (SNPs) significantly associated with soybean cyst nematode resistance (HG type 2.5.7 and HG type 1.2.3.5.6.7.), seed coat color, and seed weight

Trait Chr SNP position P value Minor allele frequency R2 of model without SNP R2 of model with SNP FDR-adjusted P value Allele effect estimate
HG 2.5.7 SCN resistance 1 18,388,403 1.02 × 10−6 0.070 0.115 0.176 0.030 47.72
1 18,388,408 1.12 × 10−6 0.070 0.115 0.176 0.030 47.27
1 18,388,378 1.36 × 10−6 0.070 0.115 0.175 0.030 46.93
1 18,388,392 1.53 × 10−6 0.068 0.115 0.174 0.030 47.02
9 35,068,146 1.80 × 10−6 0.166 0.115 0.174 0.030 48.96
1 10,061,925 4.94 × 10−6 0.071 0.115 0.168 0.070 −45.90
HG 1.2.3.5.6.7 SCN resistance 7 44,761,605 9.57 × 10−7 0.204 0.158 0.217 0.081 92.74
Seed coat color 6 9,601,167 7.95E−08 0.144 0.417 0.537 0.007 0.31
2 17,276,368 6.89 × 10−7 0.403 0.417 0.519 0.017 0.23
2 17,278,934 8.51 × 10−7 0.413 0.417 0.517 0.017 0.21
9 19,120,733 1.45 × 10−6 0.028 0.417 0.512 0.017 −0.52
2 47,163,511 1.53 × 10−6 0.106 0.417 0.512 0.017 0.62
2 17,278,931 1.64 × 10−6 0.459 0.417 0.511 0.017 −0.20
3 50,861,768 1.81 × 10−6 0.163 0.417 0.51 0.017 −0.84
3 50,928,462 1.81 × 10−6 0.163 0.417 0.51 0.017 −0.84
6 5,131,072 1.82 × 10−6 0.234 0.417 0.51 0.017 −0.49
2 17,294,139 3.25 × 10−6 0.406 0.417 0.505 0.028 0.21
Seed weighta 3 5,204,703 6.24 × 10−7 0.167 0.617 0.645 0.023 7.56
11 16,852,607 6.40 × 10−7 0.065 0.617 0.645 0.023 7.02
2 43,368,553 3.09 × 10−6 0.193 0.617 0.641 0.023 11.92
2 43,379,956 3.09 × 10−6 0.193 0.617 0.641 0.023 11.92
2 43,400,258 3.09 × 10−6 0.193 0.617 0.641 0.023 11.92
7 17,891,385 3.10 × 10−6 0.186 0.617 0.641 0.023 −5.54
3 3,306,736 3.30 × 10−6 0.198 0.617 0.641 0.023 15.77
3 3,306,784 3.30 × 10−6 0.198 0.617 0.641 0.023 15.77
3 3,307,933 3.30 × 10−6 0.198 0.617 0.641 0.023 15.77
3 3,307,946 3.30 × 10−6 0.198 0.617 0.641 0.023 15.77
3 3,307,948 3.30 × 10−6 0.198 0.617 0.641 0.023 15.77
3 3,335,111 3.30 × 10−6 0.198 0.617 0.641 0.023 15.77
2 32,146,945 3.91 × 10−6 0.193 0.617 0.641 0.024 14.21
2 32,146,953 3.91 × 10−6 0.193 0.617 0.641 0.024 14.21

aTop 15 SNPs shown