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Table 2 Non-synonymous SNPs in stress-responsive rice genes showing significant association with ecological differentiation of rice genotypes

From: SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure

Stress-responsive rice genes MSU locus IDs Major allele in upland rice genotypes Minor allele in lowland rice genotypes P value R2value
WRKY family transcription factor LOC_Os04g39570 A C 0.0012 1.00
Calcium dependent protein kinase LOC_Os01g09580 T C 0.0027 1.00
MYB family transcription factor LOC_Os02g02370 A T 0.0031 1.00
Heat Shock factor LOC_Os02g29100 C T 0.0032 1.00
Sucrose transporter LOC_Os10g26470 G A 0.0043 1.00
Pyruvate kinase LOC_Os04g58110 C T 0.0047 1.00
Soluble acid invertase LOC_Os09g06790 C T 0.0035 1.00
Cytochrome P450 LOC_Os04g40470 C T 0.0030 1.00
Elongation factor LOC_Os06g37440 C T 0.0050 1.00
Leucine-rich repeat domain LOC_Os04g19750 T C 0.0190 0.94
NBS-LRR disease resistance LOC_Os04g54780 C A 0.0290 0.91
Serine/threonine protein kinase LOC_Os09g37949 A G 0.0470 0.90
NB-ARC domain LOC_Os04g30930 A G 0.0500 0.90
40S ribosomal protein S24 LOC_Os06g40650 A G 0.0290 0.90
AP2-like ethylene responsive transcription factor LOC_Os02g40070 C G 0.0280 0.90
ABC transporter family protein LOC_Os11g05700 A C 0.0340 0.92
Zinc finger C3HC4 type family protein LOC_Os11g36560 A G 0.0460 0.90
OsWAK receptor-like protein kinase LOC_Os12g30460 G T 0.0380 0.91