GWAS and multi-omics study reveal OsJAR2 associated jasmonate biosynthesis contributes to Southern rice black-streaked dwarf virus resistance in rice

Southern rice black-streaked dwarf virus (SRBSDV), transmitted by the white-backed planthopper (WBPH), causes severe yield losses in rice across Asia. However, elite resistant germplasms and molecular defense mechanisms remain elusive, hindering breeding efforts. Screening of 195 international diverse rice accessions identified a highly resistant (up to 0% disease incidence) variety (R91), exhibiting dual resistance to SRBSDV and rice black-streaked dwarf virus (RBSDV). Multi-omics analysis revealed a rapid defense activation in R91, with an increase in Jasmonic Acid (JA) and Jasmonic Acid-Isoleucine (JA-Ile) by 5 days post-inoculation (dpi), along with upregulation of more than 2,000 defense genes. In contract, susceptible line showed declining JA and JA-Ile level along with suppressed defense responses. Time-ordered co-expression networks pinpointed that OsJAR2 (encoding a JA-Ile synthase, LOC_Os01g12160) may act as a hub of resistance molecular network. Genome wide association study (GWAS) identified a novel SRBSDV resistance quantitative trait locus (qSRBSDV1-1) co-localizing with OsJAR2, and haplotype analysis validated OsJAR2 as the candidate causal resistance gene, further providing genetic evidence for its role in SRBSDV defense. Our study identifies a highly SRBSDV-resistant rice germplasm, offering valuable genetic resource for both resistance research and breeding programs. We demonstrate that rapid JA biosynthesis activation and coordinated defense gene expression form the molecular basis of resistance in this accession. Crucially, we pinpoint OsJAR2 as a novel functional resistance gene, with its associated resistant haplotype serving as a robust molecular marker for marker-assisted selection (MAS). These findings advance our understanding of SRBSDV resistance mechanisms and provide a genetic toolkit for developing elite, disease-resistant rice varieties.