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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