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Table 3 Details of loci governing four simple and two moderately complex inherited traits in soybean identified by genome-wide association study performed using a diverse set of 553 soybean plant introductions (PIs) genotyped with the SoySNP50K iSelect BeadChip data set

From: Genetic architecture of cyst nematode resistance revealed by genome-wide association study in soybean

Trait Chromosome no. MSS position MSS P-value R2* R2** Total SNPs Significant locus
Start End
Seed coat color
Black 8 8427110 3.89E-12 0.58 0.62 19 7780581 8627848
Green 1 52253980 3.99E-12 0.24 0.31 7 52253980 52743661
Brown 15 12772149 5.70E-07 0.38 0.41 1 12772149 12772149
Yellow 1 52253980 5.80E-16 0.52 0.58 6 52249479 52717757
  8 8462762 4.40E-12 0.52 0.56 10 8227016 8627848
  6 18766611 1.04E-08 0.52 0.55 5 18118558 18766611
Flower color 13 4559799 3.13E-41 0.40 0.63 90 2493212 5074933
Pubescence color 6 18766611 8.01E-28 0.38 0.53 22 17567713 18810733
Stem growth habit 19 45000827 2.71E-31 0.38 0.56 40 44367612 45325838
Pod shattering 16 29242023 1.37E-07 0.26 0.30 6 29215338 29666971
Lodging 19 45000827 5.10E-14 0.23 0.32 11 44734359 45178132
  1. Chr. – Chromosome, MSS – Most significant SNP, *– R square of model without SNP,** – R square of model with SNP