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Table 1 Non-synonymous SNPs in stress-responsive rice genes that differentiated upland genotypes from lowland genotypes of rice

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

Functional classifications

Stress-responsive rice genes

Codon substitutions

Amino acid replacement

Types of mutation

Possible causes of altered secondary protein structure and functions

Transcription factors

WRKY family transcription factor

TAC to TCC

Tyrosine to Serine

Missense substitution

Conserved WRKY DNA binding domains and differential sequence-specific DNA binding affinity

MYB family transcription factor

GAG to GTG

Glutamic acid to Valine

Missense substitution

Conserved N-terminal tryptophan clustered Myb DNA binding domains and differential DNA binding affinity

Heat Shock factor

CGA to TGA

Glycine to Opal

Nonsense/Introduction of premature termination codon

Conserved C-terminal basic zipper signal sensing domains that senses external signals and transmit to transcription DNA binding domains of same protein

Metabolism, photosynthesis and protein synthesis related

Sucrose transporter

CGC to CAC

Arginine to Histidine

Missense substitution

Transmembrane beta-stranded domain affects apoplastic sucrose transportation by protonophores/cation symporter activity

Pyruvate kinase

CAA to TAA

Glutamine to Ochre

Nonsense/Introduction of premature termination codon

Enzyme regulatory active catalytic domain binding site with substrate (phosphoenol pyruvate) and Mn2+ ligand complexes affects allosteric mechanism of glycolysis

Soluble acid invertase

CAA to TAA

Glutamine to Ochre

Nonsense/Introduction of premature termination codon

Small conserved amino acid sequence in active domain binding site with substrate and Na+ ligand complexes regulates sucrose to hexose ratio in vacuole

Cytochrome P450

CAG to TAG

Glutamine to Amber

Nonsense/Introduction of premature termination codon

Conserved cysteine residues active domain binding site with Fe3+ ligand complexes that regulates multi-component electron transfer chains in photosynthesis

Elongation factor

CAG to TAG

Glutamine to Amber

Nonsense/Introduction of premature termination codon

A GTP-binding catalytic domain with Mg2+ ligand binding complexes affects binding of aminoacyl tRNA

Stress signal transduction

Calcium dependent Protein kinase

GTC to GCC

Valine to Alanine

Nonsense/Introduction of premature termination codon

Glycine-rich ATP conserved catalytic domain and peptide-substrate and Ca2+ ligand binding site affects phosphorylation

Resistance gene analogue (RGA)

Leucine-rich repeat domain

GTC to GCC

Valine to Alanine

Missense substitution

Dimerization of functional domain and altered ligand binding site

NBS-LRR disease resistance

TCC to TAC

Serine to Tyrosine

Missense substitution

Dimerization of functional domain and altered ligand binding site

Serine/threonine protein kinase

CAG to CGG

Glutamine to Arginine

Missense substitution

Conserved functional domain and altered ligand binding site affects phosphorylation

 

NB-ARC domain

GAT to GGT

Aspartic acid to Glycine

Missense substitution

Conserved functional domain and altered ligand binding site