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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]
       OsMYB2 [28]
       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  
qSR7 seedling survival rate 7 29,111,646 1.77E-05 0.039475464  
qSR9 seedling survival rate 9 7,106,185 4.07E-09 0.136902573 clr9 [30]