Genetic linkage and transcriptome sequencing analysis of submergence tolerance genetic characteristics in Dongxiang wild rice (DXWR)

The submergence tolerance of rice is a key factor in promoting rice live broadcasting technology and resisting flood disasters. Dongxiang wild rice (DXWR) has strong hypoxic germination and submergence tolerance during the seedling stage, but its genetic and molecular mechanisms are still unclear. Here, we report quantitative trait loci (QTLs) analysis for hypoxic germination rate (HGR), hypoxic seedling rate (HSR), budlet submergence survival rate (BSSR) and seedling sub-mergence survival rate (SSSR) using a linkage map in the backcross recombinant inbred lines (BRILs) that were derived from a cross of DXWR, and an indica cultivar, GZX49. A total of 20 QTLs related to submergence tolerance of rice were detected, explaining phenotypic variations ranging from 2% to 8.5%. Furthermore, transcriptome sequencing was performed on the seeds and seedlings of DXWR before and after flooding, and 6306 and 3226 differentially expressed genes (DEGs) were detected during seed hypoxic germination and seedling flooding, respectively. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses were con-ducted on these differentially expressed genes, revealing the mechanisms of hypoxic germination in DXWR seeds and submergence tolerance in seedlings. Perform candidate gene analysis on qHGR5.2 co-located with HGR and SSSR. These results will provide insights into the mechanism of rice submergence tolerance and provide a basis for improving rice submergence tolerance.