Detecting novel loci underlying rice blast resistance by integrating a genome-wide association study and RNA sequencing

Abstract

Rice (Oryza sativa) blast disease causes great annual yield losses and quality reductions. Limited resistance genes have been identified. Here, a genome-wide association study, together with an RNA sequencing analysis, was performed to identify novel marker–trait associations. In total, 127 associations were identified, explaining an average of 29.77% of the phenotypic variation. Five chromosomal hotspots were obtained. Moreover, 25 pleiotropic associations were associated with more than two strains. In particular, the lead single nucleotide polymorphism, seq–rs4199, close to Pi5 and Pi56(t) on chromosome 9, was associated with five different strains. In addition, 2341 nonredundant candidate genes, including 45 disease resistance-related genes, were predicted in a 200-kb genomic region for these associations. One gene, LOC_Os12g23930, overlapped a previously reported candidate resistance gene, and its relative expression level significantly decreased after inoculation. Furthermore, 683 differentially expressed rice genes, including 282 up- and 401 downregulated genes, were identified using RNA sequencing. By integrating our analyses techniques, three overlapping candidate genes, LOC_Os02g02850, LOC_Os02g41590, and LOC_Os02g41630, were obtained. The relative expression level of the former significantly increased after fungal inoculations, while the levels of the latter two significantly decreased. This work will help elucidate the molecular mechanisms of rice blast resistance.