Genome-wide association study to identify candidate genes for submergence tolerance during rice seed germination.

key messageSubmergence tolerance QTLs for rice germination were identified via a genome-wide association study, and a new causal gene, LOC_Os06g17260, was identified. Submergence stress is a major obstacle limiting the application of direct seeding in rice cultivation. Rapid bud and root growth helps plants establish a stronger growth base and improve their submergence tolerance. Therefore, mining genes for bud length (BL) and root length (RL) helps in the development of varieties that are adaptable to submergence and improve seedling emergence and yield of direct-seeded rice. In this study, a genome-wide association study of BL and RL was performed on a diverse rice collection consisting of 300 accessions. We identified a total of 37 QTLs, 13 of which had phenotypic contributions > 10%. The novel QTLs qBL6.2/qRL6.8, qBL6.3/qRL6.9, qBL6.4/qRL6.10, and qBL6.5/qRL6.11 on chromosome 6 were stably detected across BL and RL, and a total of 31 genes were detected in these four intervals. Concerning the gene annotation information and expression profiles, LOC_Os06g17090, LOC_Os06g17120, LOC_Os06g17140, LOC_Os06g17220, and LOC_Os06g17260 were selected as possible target genes. Through the validation of a knockout transgenic experiment, LOC_Os06g17260 was identified as the causal gene for submergence tolerance in rice at the germination stage. LOC_Os06g17260 encodes UDP-glucoronosyl and a UDP-glucosyl transferase domain-containing protein and contains two major haplotypes, with the Hap1 germplasm presenting greater submergence tolerance at the germination stage. These results provide new clues for exploring the molecular mechanisms that regulate submergence tolerance in rice and provide a promising source of genes for the molecular breeding of direct-seeded rice.