Abstract
<jats:p>Seed vigor (SV) is a key factor determining the success of direct seeding in rice (Oryza sativa L.), yet its genetic basis remains largely unexplored. In this study, we performed a genome-wide association study (GWAS) using 36,727 single nucleotide polymorphisms (SNPs) in a natural population of 211 rice landraces (130 indica and 81 japonica) to identify quantitative trait loci (QTLs) and candidate genes associated with SV. Twelve phenotypic indices reflecting SV under both control and natural aging conditions were evaluated. A total of 54 QTLs were identified, including 32 novel loci. Among these, 22 QTLs co-localized with previously reported SV-associated regions, validating the reliability of our results. Several genomic regions containing QTLs for multiple SV traits were detected, suggesting pleiotropic effects. A major QTL on chromosome 10, qGP10-2, which explained 11.33% of the phenotypic variation in germination percentage, was further investigated. Linkage disequilibrium decay analysis delimited a 353-kb candidate region harboring 64 genes. Expression profiling revealed that eight genes were highly expressed in dry seeds, embryos, endosperms, imbibed mature seeds, or post-germination stages. Haplotype analysis of these eight genes showed that two of them—LOC_Os10g35690 (encoding a ribosomal protein S18 domain-containing protein) and LOC_Os10g35720 (OsGRXS17)—carry distinct haplotypes between indica and japonica accessions, which precisely corresponds to the significantly higher SV values observed in indica rice. These two genes are therefore proposed as strong candidates for regulating seed vigor. This study provides new insights into the genetic architecture of seed vigor and offers valuable QTLs and candidate genes for breeding rice varieties with enhanced direct-seeding performance and seed storability.</jats:p>