Genome-wide association studies for rice seed germination under drought stress using 3VmrMLM

Improving seed germination under drought stress has the potential to increase crop yield in dry direct-seeded rice. In this study, a genome-wide association study (GWAS) was conducted to determine the genetic basis of seed germination under drought stress in a panel of 165 rice accessions using a multi-locus compressed variance-component mixed model, 3VmrMLM. A total of 33 quantitative trait nucleotides (QTNs) were identified in association with drought tolerance during seed germination. Around these QTNs, eight were found to be co-localized with known drought-related genes. Furthermore, a causal candidate gene, OsGA2ox5, which encodes a gibberellin (GA) 2-oxidase, was identified for QTN-Chr07_242906 by integrating linkage disequilibrium (LD) analysis and gene expression analysis. Knockout mutation of OsGA2ox5 resulted in delayed seed germination and retarded seedling growth under drought stress. RNA-seq analysis revealed that OsGA2ox5 regulates drought tolerance during seed germination mainly by modulating carbohydrate metabolism. Additionally, a non-synonymous coding variant in OsGA2ox5, SNP-Chr07_218893, was found to be strongly associated with drought tolerance level during seed germination. These findings provide valuable information for further exploration of novel drought-related genes and genetic improvement of rice drought tolerance in the future.