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Genome-wide association mapping of gene loci affecting disease resistance in the rice-Fusarium fujikuroi pathosystem

BACKGROUND: Rice bakanae disease has emerged as a new threat to rice production. In recent years, an increase in the occurrence and severity of bakanae disease has been reported in several areas in Asia. Although bakanae disease affects rice yield and quality, little is known about the genetics of b...

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Autores principales: Chen, Szu-Yu, Lai, Ming-Hsin, Tung, Chih-Wei, Wu, Dong-Hong, Chang, Fang-Yu, Lin, Tsung-Chun, Chung, Chia-Lin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer US 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872702/
https://www.ncbi.nlm.nih.gov/pubmed/31754813
http://dx.doi.org/10.1186/s12284-019-0337-3
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author Chen, Szu-Yu
Lai, Ming-Hsin
Tung, Chih-Wei
Wu, Dong-Hong
Chang, Fang-Yu
Lin, Tsung-Chun
Chung, Chia-Lin
author_facet Chen, Szu-Yu
Lai, Ming-Hsin
Tung, Chih-Wei
Wu, Dong-Hong
Chang, Fang-Yu
Lin, Tsung-Chun
Chung, Chia-Lin
author_sort Chen, Szu-Yu
collection PubMed
description BACKGROUND: Rice bakanae disease has emerged as a new threat to rice production. In recent years, an increase in the occurrence and severity of bakanae disease has been reported in several areas in Asia. Although bakanae disease affects rice yield and quality, little is known about the genetics of bakanae resistance in rice. The lack of large-scale screens for bakanae resistance in rice germplasm has also limited the development and deployment of resistant varieties. RESULTS: A genome-wide association study (GWAS) was conducted to identify genes/loci conferring bakanae resistance in rice. A total of 231 diverse accessions from Rice Diversity Panel 1 (RDP1) were inoculated with a highly virulent Taiwanese Fusarium fujikuroi isolate and assessed for resistance using two parameters: (1) disease severity index based on visual rating and (2) colonization rate determined by reisolation of F. fujikuroi from the basal stems of infected rice seedlings. We identified 14 quantitative trait loci (QTLs) (10 for disease severity and 4 for colonization rate), including 1 mapped for both parameters. A total of 206 candidate genes were identified within the 14 QTLs, including genes encoding leucine-rich repeat (LRR)-containing and NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) proteins, hormone-related genes, transcription factor genes, ubiquitination-related genes, and oxidase/oxidoreductase genes. In addition, a candidate QTL (qBK1.7) that co-localized with the previously identified QTLs qBK1 and qFfR1, was verified by linkage analysis using a population of 132 recombinant inbred lines derived from IR64 x Nipponbare. GWAS delineated qBK1.7 to a region of 8239 bp containing three genes. Full-length sequencing across qBK1.7 in 20 rice accessions revealed that the coding regions of two LRR-containing genes Os01g0601625 and Os01g0601675 may be associated with bakanae resistance. CONCLUSIONS: This study facilitates the exploitation of bakanae resistance resources in RDP1. The information on the resistance performance of 231 rice accessions and 14 candidate QTLs will aid efforts to breed resistance to bakanae and uncover resistance mechanisms. Quantification of the level of F. fujikuroi colonization in addition to the conventional rating of visual symptoms offers new insights into the genetics of bakanae resistance.
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spelling pubmed-68727022019-12-06 Genome-wide association mapping of gene loci affecting disease resistance in the rice-Fusarium fujikuroi pathosystem Chen, Szu-Yu Lai, Ming-Hsin Tung, Chih-Wei Wu, Dong-Hong Chang, Fang-Yu Lin, Tsung-Chun Chung, Chia-Lin Rice (N Y) Original Article BACKGROUND: Rice bakanae disease has emerged as a new threat to rice production. In recent years, an increase in the occurrence and severity of bakanae disease has been reported in several areas in Asia. Although bakanae disease affects rice yield and quality, little is known about the genetics of bakanae resistance in rice. The lack of large-scale screens for bakanae resistance in rice germplasm has also limited the development and deployment of resistant varieties. RESULTS: A genome-wide association study (GWAS) was conducted to identify genes/loci conferring bakanae resistance in rice. A total of 231 diverse accessions from Rice Diversity Panel 1 (RDP1) were inoculated with a highly virulent Taiwanese Fusarium fujikuroi isolate and assessed for resistance using two parameters: (1) disease severity index based on visual rating and (2) colonization rate determined by reisolation of F. fujikuroi from the basal stems of infected rice seedlings. We identified 14 quantitative trait loci (QTLs) (10 for disease severity and 4 for colonization rate), including 1 mapped for both parameters. A total of 206 candidate genes were identified within the 14 QTLs, including genes encoding leucine-rich repeat (LRR)-containing and NB-ARC (nucleotide-binding adaptor shared by APAF-1, R proteins, and CED-4) proteins, hormone-related genes, transcription factor genes, ubiquitination-related genes, and oxidase/oxidoreductase genes. In addition, a candidate QTL (qBK1.7) that co-localized with the previously identified QTLs qBK1 and qFfR1, was verified by linkage analysis using a population of 132 recombinant inbred lines derived from IR64 x Nipponbare. GWAS delineated qBK1.7 to a region of 8239 bp containing three genes. Full-length sequencing across qBK1.7 in 20 rice accessions revealed that the coding regions of two LRR-containing genes Os01g0601625 and Os01g0601675 may be associated with bakanae resistance. CONCLUSIONS: This study facilitates the exploitation of bakanae resistance resources in RDP1. The information on the resistance performance of 231 rice accessions and 14 candidate QTLs will aid efforts to breed resistance to bakanae and uncover resistance mechanisms. Quantification of the level of F. fujikuroi colonization in addition to the conventional rating of visual symptoms offers new insights into the genetics of bakanae resistance. Springer US 2019-11-21 /pmc/articles/PMC6872702/ /pubmed/31754813 http://dx.doi.org/10.1186/s12284-019-0337-3 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
spellingShingle Original Article
Chen, Szu-Yu
Lai, Ming-Hsin
Tung, Chih-Wei
Wu, Dong-Hong
Chang, Fang-Yu
Lin, Tsung-Chun
Chung, Chia-Lin
Genome-wide association mapping of gene loci affecting disease resistance in the rice-Fusarium fujikuroi pathosystem
title Genome-wide association mapping of gene loci affecting disease resistance in the rice-Fusarium fujikuroi pathosystem
title_full Genome-wide association mapping of gene loci affecting disease resistance in the rice-Fusarium fujikuroi pathosystem
title_fullStr Genome-wide association mapping of gene loci affecting disease resistance in the rice-Fusarium fujikuroi pathosystem
title_full_unstemmed Genome-wide association mapping of gene loci affecting disease resistance in the rice-Fusarium fujikuroi pathosystem
title_short Genome-wide association mapping of gene loci affecting disease resistance in the rice-Fusarium fujikuroi pathosystem
title_sort genome-wide association mapping of gene loci affecting disease resistance in the rice-fusarium fujikuroi pathosystem
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6872702/
https://www.ncbi.nlm.nih.gov/pubmed/31754813
http://dx.doi.org/10.1186/s12284-019-0337-3
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