Table 3 Summary of the significant SNPs detected by GWAS and the overlapping QTLs/genes reported previously
From: Identification of cold tolerance QTLs at the bud burst stage in 211 rice landraces by GWAS
QTL ID | Trait | Chr. | Peak SNPs | P value | R2 | Previous QTL/genes |
|---|---|---|---|---|---|---|
qSR2–1 | seedling survival rate | 2 | 3,379,509 | 8.99E-06 | 0.076575784 |  |
qSR2–2 | seedling survival rate | 2 | 4,435,145 | 9.70E-07 | 0.085670420 | OsWRKY71 [26] |
qSR3–1 | seedling survival rate | 3 | 10,230,171 | 3.16E-06 | 0.071228227 | qLVG3 [27] |
qSR3–2 | seedling survival rate | 3 | 10,552,889 | 1.48E-06 | 0.068345879 | qLVG3 [27] |
qSR3–3 | seedling survival rate | 3 | 11,316,517 | 1.64E-06 | 0.057976301 | qLVG3 [27] |
| Â | Â | Â | Â | Â | Â | OsMYB2 [28] |
| Â | Â | Â | Â | Â | Â | OsCIPK03 [29] |
qSR3–4 | seedling survival rate | 3 | 13,860,165 | 1.72E-08 | 0.111646171 |  |
qSR3–5 | seedling survival rate | 3 | 15,042,189 | 2.19E-08 | 0.094111949 |  |
qSR3–6 | seedling survival rate | 3 | 29,271,308 | 4.89E-05 | 0.038274826 |  |
qSR3–7 | seedling survival rate | 3 | 33,444,741 | 7.77E-06 | 0.048865413 |  |
qSR4 | seedling survival rate | 4 | 11,487,556 | 2.46E-05 | 0.03888723 | Â |
qSR7 | seedling survival rate | 7 | 29,111,646 | 1.77E-05 | 0.039475464 | Â |
qSR9 | seedling survival rate | 9 | 7,106,185 | 4.07E-09 | 0.136902573 | clr9 [30] |