Genome-Wide Association Study of Sheath Blight Resistance within a Core Collection of Rice (Oryza sativa L.)

Abstract

Sheath blight disease (ShB) is considered to be the second most important disease affecting rice, and the genetic mechanism of ShB resistance in rice is great complicated. Uncovering genetic mechanism of ShB resistance and strong resistant varieties in rice are the premise for ShB resistance improvement. A rice ShB genome-wide association study (GWAS) was performed using approximately five million SNPs within Ting’s core collection. “Early pradifice”, one typical japonica, was determined to be the most resistant variety in both 2016 and 2017. A total of 34 and four significant (p ≤ 1.93 × 10−8) SNPs were observed in 2016 and 2017, respectively. Moreover, 23 of 34 and two of four gene-based SNPs not reported in previous studies in 2016 and 2017, respectively, were identified as significantly associated with rice ShB resistance. Furthermore, we performed GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses for the genes located at a region within 10 kb of the significant SNPs. Both in 2016 and 2017, we observed that genes were uniquely enriched in the regulation of transcription and RNA processing in the category of “biological process”, plasma membrane, nucleus, integral component of membrane and cell wall in the category of “cellular component”, and ATP binding in the category of “molecular function”. The results of the present study may establish a foundation for further research investigating these elite genes and utilizing the resistant varieties in Ting’s core collection to improve rice ShB resistance.