Genome-wide association study identifies SS12 as a regulator of seed storability in rice (Oryza sativa L.)

Seed storability is crucial for rice ( Oryza sativa L.) germplasm preservation and agricultural production. Here, a genome-wide association study of 262 accessions identified qSS12 , a key quantitative trait locus controlling seed storability. Through haplotype and linkage disequilibrium analyses, we cloned the causal gene SS12 ( LOC_Os12g06440 ). Subcellular localization and autoactivation assays confirmed that SS12 functions as a nuclear-localized transcription factor. Furthermore, phenotypic evaluation of CRISPR/Cas9-edited lines demonstrated that SS12 regulates rice seed storability. Integrative RNA-seq and DAP-seq analyses identified 58 downstream target genes directly regulated by SS12 . These targets were significantly enriched in antioxidant defense and protein processing pathways, suggesting that SS12 maintains cellular protein and reactive oxygen species (ROS) homeostasis under aging stress. Domestication analysis revealed higher nucleotide diversity in the SS12 region of wild rice and a distinct selective sweep, indicating that this locus underwent strong artificial selection for enhanced seed storability during domestication. In conclusion, we characterized the key seed storability gene SS12 and propose a potential regulatory network centered on protein homeostasis and antioxidant defense. These findings provide a valuable genetic resource for breeding rice varieties with improved seed storability.