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Genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm
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...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5371361/ https://www.ncbi.nlm.nih.gov/pubmed/28355306 http://dx.doi.org/10.1371/journal.pone.0174598 |
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author | Zhang, Fan Wu, Zhi-Chao Wang, Ming-Ming Zhang, Fan Dingkuhn, Michael Xu, Jian-Long Zhou, Yong-Li Li, Zhi-Kang |
author_facet | Zhang, Fan Wu, Zhi-Chao Wang, Ming-Ming Zhang, Fan Dingkuhn, Michael Xu, Jian-Long Zhou, Yong-Li Li, Zhi-Kang |
author_sort | Zhang, Fan |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-5371361 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-53713612017-04-07 Genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm Zhang, Fan Wu, Zhi-Chao Wang, Ming-Ming Zhang, Fan Dingkuhn, Michael Xu, Jian-Long Zhou, Yong-Li Li, Zhi-Kang PLoS One Research Article 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. Public Library of Science 2017-03-29 /pmc/articles/PMC5371361/ /pubmed/28355306 http://dx.doi.org/10.1371/journal.pone.0174598 Text en © 2017 Zhang et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Zhang, Fan Wu, Zhi-Chao Wang, Ming-Ming Zhang, Fan Dingkuhn, Michael Xu, Jian-Long Zhou, Yong-Li Li, Zhi-Kang Genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm |
title | Genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm |
title_full | Genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm |
title_fullStr | Genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm |
title_full_unstemmed | Genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm |
title_short | Genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm |
title_sort | genome-wide association analysis identifies resistance loci for bacterial blight in a diverse collection of indica rice germplasm |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5371361/ https://www.ncbi.nlm.nih.gov/pubmed/28355306 http://dx.doi.org/10.1371/journal.pone.0174598 |
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