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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