Research Article: Genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm

Date Published: March 29, 2017

Publisher: Public Library of Science

Author(s): Fan Zhang, Zhi-Chao Wu, Ming-Ming Wang, Fan Zhang, Michael Dingkuhn, Jian-Long Xu, Yong-Li Zhou, Zhi-Kang Li, Zonghua Wang.


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.

Partial Text

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]. This disease is frequently prevalent in southern China and southeast Asia, resulting in heavy rice yield losses [2, 3]. Developing and deploying resistant cultivars carrying major resistance (R) genes has been the most effective approach for managing bacterial blight [4].

Our study provides new insights into the genetic basis of the evolution of bacterial blight resistance in rice. The findings reported herein may be useful for knowledge-based crop improvement. Future research will focus on validating the effects of these candidate genes and their functional variants. We will use genetic transformations and DNA insertion mutant screens to verify that these genes confer bacterial blight resistance to rice.




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