Genome-wide association mapping for identification of sheath blight resistance loci from wild rice Oryza rufipogon

Abstract

Sheath blight (ShB) caused by Rhizoctonia solani is one of the serious constraints that hamper global rice production. It causes severe yield loss of up to 69% under favorable environmental conditions. The application of chemical fungicides remains the primary approach for the management of this disease. But, overuse of chemical fungicides causes potential health and environmental risk. The use of host plant resistance is a very effective, economic, and sustainable strategy to control sheath blight disease in rice. In this report, we have evaluated 405 accessions of Oryza rufipogon for four ShB-related traits i.e. lesion height (LH), plant height (PH), relative lesion length (RLH), and disease score (DS) during the years 2015, 2016, and 2017. A total of 44,109 high-quality SNP markers on 301 accessions were employed to identify significant marker-trait associations using a genome-wide association study (GWAS). The GWAS analysis revealed a total of 22 significant SNPs associated with the ShB-related traits distributed on all the rice chromosomes except 10 and 12. Among them, eleven were associated with RLH, seven with PH, and one each with LH and DS. The SNPs on chromosomes 3 and 9 were associated with multiple traits. Furthermore, seven ShB resistance loci were also found to be co-localized with previously reported ShB resistance genes/QTLs. These findings provide valuable information to identify key SNPs associated with ShB resistance. Significantly associated SNPs could be used for introgression of ShB resistance traits into rice cultivars using marker-assisted selection.