Genome‐wide association study uncovers a novel gene responsible for rice seedling submergence tolerance

Summary Submergence tolerance is crucial for the direct seeding of rice, yet long‐term domestication and breeding have inadvertently reduced the adaptability of cultivated rice to submergence stress. Here, we identify a nucleic acid excision repair protein‐encoding gene qSHS5 as an essential regulator of seedling height under submergence through a genome‐wide association study in 322 rice accessions. Disruption of qSHS5 in mutants resulted in seedling growth inhibition under submergence, while growth remains comparable to wild‐type under normal conditions. This inhibition is primarily due to decreased cell number resulting from G1 phase cell cycle arrest. Further investigation showed that levels of reactive oxygen species (ROS), O 2 − and H 2 O 2 significantly increased, and DNA damage was aggravated in qshs5 mutants under submergence. Additionally, we find the submergence‐tolerant haplotype qSHS5 H4 has been progressively lost, while the elite haplotype qSHS5 H3 has been largely overlooked during the breeding of semi‐dwarf and high‐yield in rice. Importantly, we demonstrate that combining qSHS5 H3 with the semi‐dwarfing haplotype SD1 H1 exhibited high yield without compromising submergence tolerance, offering significant potential for future breeding programmes targeting direct seeding cultivation. This study not only identifies a novel superior allele but also provides valuable insights for future improvement of rice cultivation, particularly under climate change‐induced submergence for direct seeding.