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

TL;DR

This study finds that a gene called OsJAR2 helps rice resist a virus that causes major crop losses, offering a new tool for breeding virus-resistant rice.

Contribution

The study identifies OsJAR2 as a novel resistance gene and a functional marker for breeding virus-resistant rice.

Findings

A rice variety named R91 shows high resistance to Southern rice black-streaked dwarf virus (SRBSDV) and rice black-streaked dwarf virus (RBSDV).

OsJAR2 is a key gene in jasmonate biosynthesis and is linked to SRBSDV resistance through GWAS and haplotype analysis.

Rapid activation of jasmonic acid and defense genes is associated with resistance in R91.

Abstract

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.

The online version contains supplementary material available at 10.1186/s12864-025-12159-8.

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