Table 4.
Genome-wide significant association signals for heading date in the indica subpopulations using the LMM method in Hainan (short day conditions).
| QTL | Lead SNP | Chr. | Linkage disequilibrium interval (bp) | Distance to gene |
Indica 2012 |
Indica 2013 |
||
|---|---|---|---|---|---|---|---|---|
| P | P.V (%) | P | P.V (%) | |||||
| qHd3 | Sf0322143338 | 3 | 22079360–22143338 | 1.4E-8 | 23.3 | |||
| qHd6.3 | Sf0607922178 | 6 | 7917158–8424734 | 1.3E-9 | 22.0 | 1.1E-8 | 26.5 | |
| qHd7.1 | Sf0709158944 | 7 | 9137593–9196135 | -6.5 kb to Ghd7 | 1.2E-7 | 7.7 | 2.0E-6 | 10.0 |
| qHd7.3 | Sf0712842846 | 7 | 12774834–12894276 | 1.4E-7 | 1.1 | |||
| qHd10.2 | Sf1017100637 | 10 | 16691541–17385511 | -24.5 kb to Ehd1 | 2.9E-7 | 4.7 | ||
| qHd11 | Sf1102480009 | 11 | 2357177–2488304 | -27.5 kb to RCN1 | 3.8E-07 | 3.5 | ||
| Total estimation | 2.1E-46 | 57.7 | 1.0E-30 | 41.3 | ||||
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.