Abstract
BackgroundSheath blight (ShB), caused by Rhizoctonia solani Kühn, is one of the most destructive rice diseases. Developing ShB-resistant rice cultivars represents the most economical and environmentally sound strategy for managing ShB.ResultsTo characterize the genetic basis for ShB resistance in rice, we conducted association studies for traits related to ShB resistance, namely culm length (CL), lesion height (LH), and relative lesion height (RLH). Combined a single locus genome-wide scan and a multi-locus method using 2,977,750 single-nucleotide polymorphisms to analyse 563 rice accessions, we detected 134, 562, and 75 suggestive associations with CL, LH, and RLH, respectively. The adjacent signals associated with RLH were merged into 27 suggestively associated loci (SALs) based on the estimated linkage disequilibrium blocks. More than 44% of detected RLH-SALs harboured multiple QTLs/genes associated with ShB resistance, while the other RLH-SALs were putative novel ShB resistance loci. A total of 261 ShB resistance putative functional genes were screened from 23 RLH-SALs according to bioinformatics and haplotype analyses. Some of the annotated genes were previously reported to encode defence-related and pathogenesis-related proteins, suggesting that quantitative resistance to ShB in rice is mediated by SA- and JA-dependent signalling pathways.ConclusionsOur findings may improve the application of germplasm resources as well as knowledge-based ShB management and the breeding of ShB-resistant rice cultivars.
Highlights
Sheath blight (ShB), caused by Rhizoctonia solani Kühn, is one of the most destructive rice diseases
The 563 rice accessions were classified into the following three well-known subgroups: Xian (224 accessions), Geng (237 accessions), and Aus (102 accessions) (Additional file 1: Table S1). These results suggested that the accessions used as a covariate within the genome-wide association study (GWAS) model in this study exhibited an obvious subpopulation structure
We conducted a large-scale GWAS based on a rice core collection and approximately 3 million single nucleotide polymorphisms (SNPs) to dissect the genetic mechanisms underlying quantitative resistance to R. solani and to identify novel loci and alleles associated with resistance
Summary
Sheath blight (ShB), caused by Rhizoctonia solani Kühn, is one of the most destructive rice diseases. Sheath blight (ShB), caused by Rhizoctonia solani Kühn (R. solani), is one of the most destructive rice diseases (Zheng et al 2013). This disease, which is prevalent in East Asia and the southern USA (Chen et al 2012; Prasad and Eizenga 2008), results in heavy rice yield losses when nitrogen fertilizers are extensively applied (Savary et al 1995).
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