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Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development

BACKGROUND: Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five...

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Autores principales: Maldonado dos Santos, João Vitor, Ferreira, Everton Geraldo Capote, Passianotto, André Luiz de Lima, Brumer, Bruna Bley, Santos, Adriana Brombini Dos, Soares, Rafael Moreira, Torkamaneh, Davoud, Arias, Carlos Alberto Arrabal, Belzile, François, Abdelnoor, Ricardo Vilela, Marcelino-Guimarães, Francismar Corrêa
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6824049/
https://www.ncbi.nlm.nih.gov/pubmed/31672122
http://dx.doi.org/10.1186/s12864-019-6139-6
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author Maldonado dos Santos, João Vitor
Ferreira, Everton Geraldo Capote
Passianotto, André Luiz de Lima
Brumer, Bruna Bley
Santos, Adriana Brombini Dos
Soares, Rafael Moreira
Torkamaneh, Davoud
Arias, Carlos Alberto Arrabal
Belzile, François
Abdelnoor, Ricardo Vilela
Marcelino-Guimarães, Francismar Corrêa
author_facet Maldonado dos Santos, João Vitor
Ferreira, Everton Geraldo Capote
Passianotto, André Luiz de Lima
Brumer, Bruna Bley
Santos, Adriana Brombini Dos
Soares, Rafael Moreira
Torkamaneh, Davoud
Arias, Carlos Alberto Arrabal
Belzile, François
Abdelnoor, Ricardo Vilela
Marcelino-Guimarães, Francismar Corrêa
author_sort Maldonado dos Santos, João Vitor
collection PubMed
description BACKGROUND: Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs. RESULTS: We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R(2) = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency. CONCLUSIONS: Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression.
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spelling pubmed-68240492019-11-06 Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development Maldonado dos Santos, João Vitor Ferreira, Everton Geraldo Capote Passianotto, André Luiz de Lima Brumer, Bruna Bley Santos, Adriana Brombini Dos Soares, Rafael Moreira Torkamaneh, Davoud Arias, Carlos Alberto Arrabal Belzile, François Abdelnoor, Ricardo Vilela Marcelino-Guimarães, Francismar Corrêa BMC Genomics Research Article BACKGROUND: Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs. RESULTS: We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R(2) = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency. CONCLUSIONS: Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression. BioMed Central 2019-10-31 /pmc/articles/PMC6824049/ /pubmed/31672122 http://dx.doi.org/10.1186/s12864-019-6139-6 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. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Maldonado dos Santos, João Vitor
Ferreira, Everton Geraldo Capote
Passianotto, André Luiz de Lima
Brumer, Bruna Bley
Santos, Adriana Brombini Dos
Soares, Rafael Moreira
Torkamaneh, Davoud
Arias, Carlos Alberto Arrabal
Belzile, François
Abdelnoor, Ricardo Vilela
Marcelino-Guimarães, Francismar Corrêa
Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development
title Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development
title_full Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development
title_fullStr Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development
title_full_unstemmed Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development
title_short Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development
title_sort association mapping of a locus that confers southern stem canker resistance in soybean and snp marker development
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6824049/
https://www.ncbi.nlm.nih.gov/pubmed/31672122
http://dx.doi.org/10.1186/s12864-019-6139-6
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