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
| 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 |
Chr. – Chromosome, MSS – Most significant SNP, *– R square of model without SNP,** – R square of model with SNP