OsSV5 positively regulates rice seed vigor

High-vigor seeds are fundamental to ensuring high-quality seedling establishment in rice ( Oryza sativa L.) and play a key role in reducing cultivation costs and improving yield. To elucidate the genetic basis of rice seed vigor, we performed a genome-wide association study (GWAS) on vigor-related traits using 237 accessions from the 3K Rice Core Collection, identifying 16 quantitative trait loci (QTL). Among these, four QTLs identified in the present study— qOsGR5 (germination rate), qOsGP5 (germination potential), qOsGI5 (germination index), and qOsSS5 (seed storability)—were found to co-localize at a single locus on chromosome 5. Given its pleiotropic association with these vigor-related traits, this locus was designated qOsSV5 (rice seed vigor on chromosome 5). Candidate gene analysis preliminarily identified the bHLH transcription factor Os05g0541400 as the corresponding gene for qOsSV5 . Knockout of OsSV5 significantly reduced seed vigor and led to a marked increase in reactive oxygen species (ROS) accumulation in seeds. Domestication analysis indicated that OsSV5 has undergone strong artificial selection in japonica rice. Haplotype analysis revealed three haplotypes of OsSV5 , among which the dominant OsSV5 Hap3 was associated with high seed vigor. This favorable haplotype has been widely utilized in rice breeding programs in southern China. Collectively, our findings demonstrate that OsSV5 is a key regulator of rice seed vigor and that its dominant haplotype has been extensively applied in breeding practice.