Identification of candidate genes for deep-sowing tolerance in rice by genome-wide association study and transcriptome sequencing.

Direct-seeded rice is of great significance for ensuring food security. The hypoxic conditions under deep sowing impose significant abiotic stress to severely inhibit seed germination and seedling emergence in direct-seeded rice. Improvement of rice tolerance to deep-sowing germination stress is critical for promoting the seedling and grain yield of direct-seeded rice. In this study, we employed 276 rice germplasms to investigate the hypoxic germination (HG)-related traits through genome-wide association study (GWAS). Transcriptome profiling was conducted on germplasms with strong and weak HG tolerance under both deep-sowing and control conditions. GWAS identified 76 HG-associated genes, among which 27 genes were also detected by transcriptome profiling. Gene functional annotation and haplotype analysis screened four important candidate genes (LOC_Os01g51870, LOC_Os03g11510, LOC_Os05g01440, and LOC_Os07g35350) related to HG under deep sowing. The findings establish a genetic framework for improving HG tolerance in rice under deep sowing through molecular breeding strategies.