Genome-wide association analysis reveals novel genetic loci involved in rice brown spot resistance

Rice brown spot (BS) substantially impacts both yield and grain quality of rice, while research on this disease remains relatively limited compared to some major rice diseases like rice blast and rice sheath blight.

In our study, 529 rice accessions were evaluated for BS resistance during two growing seasons (October 2021 and March 2022), resulting in the identification of 93 accessions that consistently exhibited resistance (R) or high resistance (HR) to BS across both seasons. Among these, 5 accessions consistently displayed high resistance (HR) grade in both seasons. Additionally, GWAS analysis was performed on the BS resistant level gathered from 529 accessions across two distinct seasons, revealing 52 significant single-season identified QTLs, 11 co-located QTLs across two seasons, and 5 algorithm co-located QTLs. Notably, 13 of these QTLs overlapped with previous studies, including the significant BS resistance QTL, qBS11. Haplotype analysis within the candidate genes located in these essential intervals led to the identification of 5 potential candidate genes (LOC_Os03g40194, LOC_Os05g48660, LOC_Os02g08440, LOC_Os11g38000, LOC_Os08g06380) correlated with BS resistance. Moreover, the varying response of these 5 genes in 'Huilongzao No.1' (resistant variety) and 'ChangQi' (susceptible variety) was analyzed through qPCR analysis, suggesting their potential involvement in diverse BS resistance mechanisms.

This study provides valuable germplasm resources and identifies key candidate QTLs and genes for BS resistance research, bridging the gap in the limited identification of genetic markers associated with this disease. These findings establish a critical foundation for advancing future research into BS resistance mechanisms and breeding strategies.