Table 1. Significant markers associated with IDC in the population of soybean.
| Chromosome | Position | –log10 (p-value) | Reference Allele | Variant Allele | R2 § | MAF§§ | Mean Difference | Additive Effect (Variant allele) | Included in stepwise regression§§§ |
| Gm02 | 46,939,135 | 3.784** | A | T | 5.20 | 21.48 | 0.26 | −0.13 | |
| Gm03 | 44,927,455 | 4.165** | A | G | 15.20 | 38.89 | 0.37 | −0.19 | |
| Gm03 | 44,930,187 | 4.165** | A | T | 15.20 | 38.89 | 0.37 | −0.19 | |
| Gm03 | 44,970,860 | 4.275** | A | G | 14.42 | 39.26 | 0.36 | −0.18 | |
| Gm03 | 44,985,022 | 4.165** | G | A | 15.20 | 38.89 | 0.37 | −0.19 | |
| Gm03 | 45,031,929 | 5.127*** | T | C | 15.77 | 38.89 | 0.38 | −0.19 | x |
| Gm03 | 45,038,912 | 3.684** | C | T | 14.71 | 39.26 | 0.36 | −0.18 | |
| Gm03 | 45,107,141 | 3.905** | C | A | 13.87 | 45.56 | 0.35 | −0.17 | |
| Gm03 | 45,343,317 | 3.689** | G | T | 17.28 | 42.59 | 0.39 | −0.19 | |
| Gm03 | 45,343,612 | 4.231** | A | T | 18.85 | 41.48 | 0.41 | −0.20 | |
| Gm05 | 8,817,714 | 3.912** | G | A | 10.81 | 49.26 | 0.30 | 0.15 | |
| Gm05 | 8,823,135 | 4.617*** | G | A | 11.43 | 49.63 | 0.31 | 0.16 | |
| Gm05 | 8,877,264 | 3.855** | G | T | 8.30 | 45.93 | 0.27 | 0.13 | x |
| Gm05 | 17,397,118 | 3.704** | G | A | 0.08 | 39.63 | 0.03 | 0.01 | |
| Gm05 | 17,397,130 | 3.704** | T | C | 0.08 | 39.63 | 0.03 | 0.01 | |
| Gm05 | 17,397,135 | 3.704** | C | T | 0.08 | 39.63 | 0.03 | 0.01 | |
| Gm07 | 6,397,319 | 3.961** | C | T | 8.80 | 25.56 | 0.32 | −0.16 | x |
| Gm07 | 6,405,421 | 3.961** | T | C | 8.80 | 25.56 | 0.32 | −0.16 | |
| Gm07 | 6,540,541 | 4.128** | G | A | 8.10 | 26.30 | 0.30 | −0.15 | |
| Gm07 | 6,575,306 | 3.961** | A | G | 8.80 | 25.56 | 0.32 | −0.16 | |
| Gm11 | 530,116 | 4.401*** | A | G | 4.73 | 8.89 | 0.35 | 0.18 | x |
| Gm11 | 530,117 | 4.401*** | A | C | 4.73 | 8.89 | 0.35 | 0.18 | |
| Gm11 | 530,118 | 4.401*** | G | T | 4.73 | 8.89 | 0.35 | 0.18 | |
| Gm12 | 20,406,669 | 3.697** | T | C | 0.02 | 20.74 | 0.01 | 0.01 | |
| Gm15 | 21,422,057 | 4.152** | A | G | 2.10 | 20.37 | 0.17 | 0.08 | |
| Gm16 | 27,300,116 | 3.779** | T | G | 4.80 | 8.52 | 0.36 | 0.18 | x |
| Gm17 | 25,859,992 | 4.322** | T | C | 0.66 | 6.67 | 0.15 | 0.08 | x |
| Gm17 | 25,859,995 | 4.322** | T | C | 0.66 | 6.67 | 0.15 | 0.08 | |
| Gm18 | 15,905,372 | 3.781** | T | C | 3.25 | 28.52 | 0.18 | 0.09 | |
| Gm18 | 28,141,888 | 3.786** | G | A | 3.78 | 22.59 | 0.22 | 0.11 | x |
| Gm18 | 59,284,729 | 4.006** | C | T | 0.70 | 45.93 | 0.08 | 0.04 | |
| Gm19 | 34,914,546 | 3.769** | A | G | 0.81 | 5.19 | 0.19 | 0.09 | |
| Gm19 | 40,193,564 | 3.955** | C | A | 15.62 | 44.07 | 0.37 | −0.18 | x |
***Significant at 0.01 percentile (4.0E-05).
**Significant at 0.1 percentile (2.1E-04).
§
R2– Calculated using a simple linear regression and is represented as percentage.
§§
MAF = Minor Allele Frequency.
§§§
The markers that have an ‘x’ are included in stepwise regression. All other significant markers are in LD with one of these eight markers. This is the subset of markers around which QTLs were identified, and allelic combinations that have applications for MAS are characterized.