Zhang F, Wu ZC, Wang MM, Zhang F, Dingkuhn M, Xu JL, Zhou YL, Li ZK.

PLoS One. 2017 Mar 29;12(3):e0174598. doi: 10.1371/journal.pone.0174598. eCollection 2017.

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.

See https://www.ncbi.nlm.nih.gov/pubmed/28355306

Figure 1: Susceptible and resistant reactions of a whole population and six subpopulations of 172 indica accessions inoculated with representative strains of six Xanthomonas oryzae pv. oryzae (Xoo) races from China and the Philippines.

(A) Hierarchical cluster of accessions and races based on lesion length (LL). (B) Number of accessions in the following reactions to six Xoo races: resistant (LL < 5 cm), moderately resistant (5 cm ≤ LL < 10 cm), moderately susceptible (10 cm ≤ LL < 15 cm), and susceptible (LL ≥ 15 cm). (C) Boxplots for LLs following infections by six Xoo races in three indica subgroups divided by population structure analysis results. Box edges represent the 0.25 and 0.75 quantiles with median values indicated by bold lines. ‘***’ refers to a significant difference in the average LLs among the indica subgroups (p < 0.001). We used the following Xoo races: C5 (strain GD1358) and GV (strain V) from China, and P1 (strain PXO61), P3c (strain PXO340), P9a (strain PXO339), and P6 (strain PXO99) from the Philippines.