Genetic and Molecular Analysis of Anaerobic Germination in Rice

In this research, 153 diverse rice accessions and 144 recombinant inbred lines (RILs) were screened for their responses to submergence at germination stage. Differential anaerobic response was observed between Japonica and Indica varieties. Total 88 SNPs identified from genome-wide association studies (GWAS) were associated with anaerobic germination, and 10 genomic regions were repeatedly detected in this study and previous bi-parental QTL studies. A unique and strong signal explaining ~30% of the phenotypic variation was only detected in the RILs population. GWAS detected phenotype-genotype association with higher resolution, while bi-parental mapping was able to identify subpopulation-related variants not captured by GWAS. This study demonstrated these two approaches are complementary for dissecting the genetic architecture of complex traits in rice. By comparative transcriptomic analysis in different rice genotypes with contrasting tolerance to submergence, we identified a core set of genes being differentially regulated under submergence between tolerant and sensitive rice genotypes. These differential modulations could contribute to the fundamental tolerance in the moderate tolerant and tolerant rice genotypes. Rare allele-specific gene regulations and genotype-specific adaptive mechanisms could further promote the submergence tolerance in those genotypes with extremely adaptive phenotype. Through genetic and comparative transcriptomic aspects, we expected to have more comprehensive insights about how rice seedlings of different genotypes to germinate and survive under the oxygen/energy deficit led by submergence and utilize the knowledge in the improvement of submergence tolerance in modern rice cultivars.