Loci and alleles for submergence responses revealed by GWAS and transcriptional analysis in rice

The low seedling rate of rice caused by submergence in the process of rice direct seeding has always been an important factor limiting the popularization of rice direct seeding technology. Improving the tolerance of rice to submergence stress will benefit the production of rice and the promotion of direct seeding technology. In this study, we determined the submergence coleoptile length (SCL), submergence shoot length (SSL), and submergence tolerance index (STI) of 166 different cultivated rice seedlings as the phenotypes. Through the genome-wide association analysis (GWAS) of SCL, SSL, and STI, we found multiple quantitative trait locus (QTL) locations, including nine reported QTL locations. To narrow down the candidate gene numbers, we combined data from GWAS, transcriptomic analysis, gene function annotation, and reported QTL locations, and 50 candidate genes for submergence stress were obtained. Some reported genes had been firstly found to play certain roles in submergence-mediated growth response. Combining with reported RNA-seq data and expression profile data, we focused on four adjacent genes (LOC_Os11g47550, LOC_Os11g47570, LOC_Os11g47590, and LOC_Os11g47610) located in qAG11. RNA-seq and expression profile suggested the expression of these genes in sensitive and tolerant types differs hundreds of times (146~510 fold). Based on the diverse germplasms, we determined the natural haplotype of these genes. The haplotype analysis of these four genes showed a large genetic difference between indica and japonica. These results help us to better understand the molecular mechanism of natural variations in submergence tolerance among diverse germplasms and provide materials and new genes for further selection of new submergence tolerance varieties.