Table 3.
Top highest genome-wide significant association signals of agronomic traits using EMMAX
| Trait | Chr. | Position (IRGSP 1.0) | Reference allele | Alternative allele | Alternative allele frequency | -log10(P) | R2 (%)a | Candidate/known geneb |
|---|---|---|---|---|---|---|---|---|
| Grain width | 1 | 11,789,024 | C | A | 0.77 | 6.29 | 9.41 | |
| Heading days | 2 | 3,970,385 | G | A | 0.05 | 6.20 | 11.54 | |
| 3 | 32,824,935 | T | A | 0.05 | 6.21 | 8.57 | CK1 [29] | |
| 3 | 32,824,941 | C | G | 0.05 | 6.08 | 10.75 | CK1 [29] | |
| 4 | 463,322 | G | A | 0.95 | 7.86 | 12.86 | ||
| 4 | 463,371 | G | A | 0.94 | 7.41 | 10.97 | ||
| 8 | 15,918,110 | G | A | 0.05 | 6.21 | 7.42 | ||
| 8 | 15,918,112 | C | T | 0.05 | 6.10 | 4.38 | ||
| 9 | 18,628,054 | T | C | 0.13 | 6.04 | 6.87 | ||
| Seed set rate | 4 | 31,539,937 | A | G | 0.18 | 7.35 | 9.45 | LOC_Os04g52940.1 |
| 7 | 7,918,286 | G | A | 0.07 | 6.16 | 5.21 | ||
| 7 | 8,178,284 | A | G | 0.12 | 6.47 | 3.15 | ||
| 7 | 8,299,577 | G | A | 0.07 | 6.33 | 14.26 | ||
| 7 | 8,390,152 | C | T | 0.07 | 6.08 | 5.27 | ||
| 7 | 8,390,155 | C | T | 0.07 | 6.09 | 8.25 | ||
| 7 | 8,447,659 | T | C | 0.09 | 6.45 | 9.64 | LOC_Os07g14800.1 |
Note: aR2 represents the genetic variants explained by the significant SNPs. bGene ID of MSU rice genome annotation project (http://rice.plantbiology.msu.edu/)