Genome-wide association analysis of resistance to rice false smut

Abstract

Rice false smut (RFS), caused by Ustilaginoidea virens, is one of the most destructive grain diseases in rice production worldwide. Hence, to increase the ability of rice resistance to U. virens is a major breeding goal of rice breeders. However, it is difficult to evaluate rice resistance to U. virens. Hence, to clarify the RFS-resistance genetic mechanism is of great significance. In this study, a diversity panel landrace comprising of 315 accessions was identified for resistance against U. virens at reproductive stage in 2017 and 2018. Totally, 58 significant SNPs were distributed on the rice whole genome except chromosome 7, and 3 SNPs associated with three RFS-related traits were identified in 2 years. Haplotype block structure analysis predicted that a total of 15 candidate genes for U. virens resistance were screened based on significant SNPs with minimum P value (− log10P = 13.86). Of which, LOC_Os01g15580, a plant NBS-LRR protein coding gene near the significant SNP chr01_8738751 (12.3 kb), was considered a candidate for key resistance factor in the disease. These findings might provide a new insight into the genetic basis of resistance to rice false smut.