Table 3.
Genome-wide significant association signals for heading date in indica and japonica subpopulations using the LMM method in Wuhan (long day conditions).
| QTL | Lead SNP | Chr. | Linkage disequilibrium interval (bp) | Distance to gene |
Indica 2013 |
Indica 2014 |
Japonica 2013 |
Japonica 2014 |
||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| P | P.V (%) | P | P.V (%) | P | P.V (%) | P | P.V (%) | |||||
| qHd4 | Sf0403512804 | 4 | 3145576–3733894 | 1.8E-7 | 26.1 | |||||||
| qHd6.1 | Sf0602312322 | 6 | 2311322–2931955 | 78.2 kb to Hd17 | 1.6E-6 | 19.7 | 4.4E-7 | 18.7 | ||||
| qHd6.2 | Sf0602663020 | 6 | 2396433–2733565 | 8.0E-7 | 13.2 | 4.4E-6 | 16.8 | |||||
| qHd7.1 | Sf0709177919 | 7 | 9137593–9196135 | -25.5 kb to Ghd7 | 5.7E-7 | 7.3 | 1.1E-6 | 7.1 | ||||
| qHd7.2 | Sf0711412802 | 7 | 11316108–11898697 | 3.1E-7 | 16.6 | |||||||
| qHd8 | Sf0804089477 | 8 | 3942483–4245642 | 3.5E-8 | 9.5 | |||||||
| qHd10.1 | Sf1001634949 | 10 | 1596335–1634949 | 2.2E-7 | 7.4 | |||||||
| Total estimation | 7.2E-19 | 27.1 | 4.0E-25 | 35.3 | 3.8E-16 | 39.4 | 3.2E-15 | 40.8 | ||||
Linkage disequilibrium interval means the linkage disequilibrium (r2 > 0.2) extended genome region surrounding the lead SNP. P is P-value estimated in LMM, P.V (%) is phenotype variance explained by the QTL in percent.