Determination of adaptive mechanisms for flash flooding tolerance in Nepalese cultivated rice genepool based on morpho-physiological and molecular analysis

Flooding is notorious to rice (Oryza sativa L.) cultivation at any stages threatening the life of >100 millions people in Asia annually. Compare to other cereals rice has unusual capacity to tolerate both short and long term flooding attributed to coordinated efforts of several morphological, anatomical, biochemical and action of adaptive genes. In this study three hundred and thirteen Nepalese rice landrace collected from diverse geographic regions were completely submerged for 14 days. Status of SublA gene was monitored in tolerant rice accessions identified here. Diverse rice accession possessed differential elongation growth response and their survival ability ranged from 0-100%. Some of the rice accessions performed better than the tolerant check; FR13A. Monitoring of SublA gene presence revealed that some of the tolerant rice accessions are lacking the SublA gene and SublA-1 allele. Four accessions; Bhaatsaar, Kariyaparewa pakha, Sauthari and Karangi possessed the better survival response than the FR13A and remaining accessions had poorer response. Among tolerant accessions; Kariyaparewa pakha and Sauthari were lacking the SublA-1 allele though followed the quiescence growth response. Interestingly, eight rice accessions with SublA-1 allele was found to be intolerant to 14 days of complete submergence. Unlike FR13A all the tolerant and intolerant rice accessions displayed the bleaching of chlorophyll pigment resulting the lower SPAD reading. The detailed morpho-physiological and molecular analysis unveiled that both tolerant and intolerant rice accessions harbored SublA gene and adapt the both quiescence and escape strategies in response to flash flooding. Beside SublA gene, there might be participation of other stress responsive factors that probably functions in close coordination with Subl haplotype. In conclusion SublA-1 alone is not a major contributing factor to confer submergence tolerance in diverse rice accessions thus haplotype based profiling followed by cloning and sequencing is suggested.