Variation in expression of Sub1 gene confers differential response to submergence tolerance in rice (Oryza sativa L.)

A cluster of three ethylene response factor (ERF) like genes at the Sub1 locus has been identified from rice variety FR13A that confers tolerance to submergence for about 14 days. Restriction digestion-based haplotype variations among 11 rice accessions were analyzed to generate polymorphisms at Sub1C and Sub1A loci. Considering different combinations of SNPs (haplotype), four haplotypes: A1C1, A1C2, A2C2 and A0C2 were detected. Further, using semi-quantitative RT-PCR - Sub1A and Sub1C transcripts in different haplotypes were interpreted in respect with stem elongation and survival for understanding mechanism of submergence tolerance. Expression variations in Sub1 genes in relation with duration of submergence, haplotype diversity and an interaction of loci were found. Differential expression of Sub1A and Sub1C affected the stem elongation and survival of different haplotypes differentially. In tolerant varieties (A1C1 haplotype, IR40931), the highest expressed gene was Sub1A; while expression of Sub1C was lower. Over-expression of Sub1A gene in tolerant varieties, suppressed the stem elongation under submergence, which improved the level of submergence tolerance. In susceptible cultivar (Fulkari), the highest-expressed gene was Sub1C, while the Sub1A was not expressed which showed higher susceptibility. In moderately tolerant varieties (Kottamali), both Sub1A and Sub1C gene transcripts were up-regulated by submergence and higher level of both Sub1A and Sub1C genes transcripts. The varieties in A2C2 haplotype showed moderate level of tolerance without the Sub1A1 allele and a distinct novel mechanism favored the expression of both the Sub1A and Sub1C alleles that confer higher tolerance under complete submergence.