Abstract
Bacterial blight, which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating rice diseases worldwide. The development and use of disease-resistant cultivars have been the most effective strategy to control bacterial blight. Identifying the genes mediating bacterial blight resistance is a prerequisite for breeding cultivars with broad-spectrum and durable resistance. We herein describe a genome-wide association study involving 172 diverse Oryza sativa ssp. indica accessions to identify loci influencing the resistance to representative strains of six Xoo races. Twelve resistance loci containing 121 significantly associated signals were identified using 317,894 single nucleotide polymorphisms, which explained 13.3–59.9% of the variability in lesion length caused by Xoo races P1, P6, and P9a. Two hotspot regions (L11 and L12) were located within or nearby two cloned R genes (xa25 and Xa26) and one fine-mapped R gene (Xa4). Our results confirmed the relatively high resolution of genome-wide association studies. Moreover, we detected novel significant associations on chromosomes 2, 3, and 6–10. Haplotype analyses of xa25, the Xa26 paralog (MRKc; LOC_Os11g47290), and a Xa4 candidate gene (LOC_11g46870) revealed differences in bacterial blight resistance among indica subgroups. These differences were responsible for the observed variations in lesion lengths resulting from infections by Xoo races P1 and P9a. Our findings may be relevant for future studies involving bacterial blight resistance gene cloning, and provide insights into the genetic basis for bacterial blight resistance in indica rice, which may be useful for knowledge-based crop improvement.
Highlights
Bacterial blight, which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases of cultivated rice (Oryza sativa L.) in tropical and temperate regions worldwide [1]
Distinct differences in bacterial blight resistance among indica rice subgroups We conducted a genome-wide association study (GWAS) involving 172 global indica accessions infected by representative strains of six Xoo races from China and the Philippines to analyze the genetic basis of bacterial blight resistance in rice, and detected two hotspot regions associated with Xoo resistance
Only two single nucleotide polymorphisms (SNPs) with weak but significant signals associated to resistance for P6 were detected (Table 1 and Fig 2), no any SNPs significantly associated resistance for Xoo races P3c, C5, and GV was identified in the tested rice accessions due to limited phenotypic variation (Fig 1), suggesting lack of R gene/QTL with large effect on resistance for these races in the association panel
Summary
Bacterial blight, which is caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases of cultivated rice (Oryza sativa L.) in tropical and temperate regions worldwide [1]. Based on analyses of phenotypic responses to Xoo races and molecular mapping results for identified genes, 41 R genes (i.e., 29 dominant and 12 recessive genes) conferring resistance to bacterial blight have been registered in the Oryzabase database (http://www.shigen.nig.ac.jp/rice/ oryzabase/gene/list). Most of these genes are derived from Oryza sativa ssp. Quantitative trait loci (QTLs) for resistance to bacterial blight caused by different Xoo isolates have been reported [24, 25]
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