Genome-wide association studies in sunflower : towards sclerotinia sclerotiorum and diaporthe/phomopsis resistance breeding

Autores
Filippi, Carla Valeria; Corro Molas, Andres Ezequiel; Dominguez, Matías; Colombo, Denis Nahuel; Heinz, Nicolás; Troglia, Carolina Beatriz; Maringolo, Carla Andrea; Quiroz, Facundo Jose; Alvarez, Daniel; Lia, Veronica Viviana; Paniego, Norma Beatriz
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Diseases caused by necrotrophic fungi, such as the cosmopolitan Sclerotinia sclerotiorum and the Diaporthe/Phomopsis complex, are among the most destructive diseases of sunflower worldwide. The lack of complete resistance combined with the inefficiency of chemical control makes assisted breeding the best strategy for disease control. In this work, we present an integrated genome-wide association (GWA) study investigating the response of a diverse panel of sunflower inbred lines to both pathogens. Phenotypic data for Sclerotinia head rot (SHR) consisted of five disease descriptors (disease incidence, DI; disease severity, DS; area under the disease progress curve for DI, AUDPCI, and DS, AUDPCS; and incubation period, IP). Two disease descriptors (DI and DS) were evaluated for two manifestations of Diaporthe/Phomopsis: Phomopsis stem canker (PSC) and Phomopsis head rot (PHR). In addition, a principal component (PC) analysis was used to derive transformed phenotypes as inputs to a univariateGWA (PC-GWA). Genotypic data comprised a panel of 4269 single nucleotide polymorphisms (SNP), generated via genotyping-by-sequencing. The GWA analysis revealed 24 unique marker–trait associations for SHR, 19 unique marker–trait associations for Diaporthe/Phomopsis diseases, and 7 markers associated with PC1 and PC2. No common markers were found for the response to the two pathogens. Nevertheless, epistatic interactions were identified between markers significantly associated with the response to S. sclerotiorum and Diaporthe/Phomopsis. This suggests that, while the main determinants of resistance may differ for the two pathogens, there could be an underlying common genetic basis. The exploration of regions physically close to the associated markers yielded 364 genes, of which 19 were predicted as putative disease resistance genes. This work presents the first simultaneous evaluation of two manifestations of Diaporthe/Phomopsis in sunflower, and undertakes a comprehensive GWA study by integrating PSC, PHR, and SHR data. The multiple regions identified, and their exploration to identify candidate genes, contribute not only to the understanding of the genetic basis of resistance, but also to the development of tools for assisted breeding.
Instituto de Biotecnología
Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Filippi, Carla Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Corro Molas, Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Anguil. Agencia de Extensión Rural General Pico; Argentina
Fil: Dominguez, Matías. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino; Argentina
Fil: Colombo, Denis Nahuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Anguil; Argentina
Fil: Heinz, N. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Troglia, Carolina Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina
Fil: Maringolo, Carla Andrea. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina
Fil: Quiroz, Facundo Jose. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina
Fil: Alvarez, Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Lia, Veronica Viviana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Lia, Veronica Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Lia, Veronica Viviana. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Paniego, Norma Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fuente
Genes 13 (12) : 2357 (Diciembre 2022)
Materia
Sunflowers
Diaporthe
Phomopsis
Genomes
Girasol
Helianthus annuus
Sclerotinia sclerotiorum
Diaporthe helianthi
Genomas
GWAS
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/13697
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spelling Genome-wide association studies in sunflower : towards sclerotinia sclerotiorum and diaporthe/phomopsis resistance breedingFilippi, Carla ValeriaCorro Molas, Andres EzequielDominguez, MatíasColombo, Denis NahuelHeinz, NicolásTroglia, Carolina BeatrizMaringolo, Carla AndreaQuiroz, Facundo JoseAlvarez, DanielLia, Veronica VivianaPaniego, Norma BeatrizSunflowersDiaporthePhomopsisGenomesGirasolHelianthus annuusSclerotinia sclerotiorumDiaporthe helianthiGenomasGWASDiseases caused by necrotrophic fungi, such as the cosmopolitan Sclerotinia sclerotiorum and the Diaporthe/Phomopsis complex, are among the most destructive diseases of sunflower worldwide. The lack of complete resistance combined with the inefficiency of chemical control makes assisted breeding the best strategy for disease control. In this work, we present an integrated genome-wide association (GWA) study investigating the response of a diverse panel of sunflower inbred lines to both pathogens. Phenotypic data for Sclerotinia head rot (SHR) consisted of five disease descriptors (disease incidence, DI; disease severity, DS; area under the disease progress curve for DI, AUDPCI, and DS, AUDPCS; and incubation period, IP). Two disease descriptors (DI and DS) were evaluated for two manifestations of Diaporthe/Phomopsis: Phomopsis stem canker (PSC) and Phomopsis head rot (PHR). In addition, a principal component (PC) analysis was used to derive transformed phenotypes as inputs to a univariateGWA (PC-GWA). Genotypic data comprised a panel of 4269 single nucleotide polymorphisms (SNP), generated via genotyping-by-sequencing. The GWA analysis revealed 24 unique marker–trait associations for SHR, 19 unique marker–trait associations for Diaporthe/Phomopsis diseases, and 7 markers associated with PC1 and PC2. No common markers were found for the response to the two pathogens. Nevertheless, epistatic interactions were identified between markers significantly associated with the response to S. sclerotiorum and Diaporthe/Phomopsis. This suggests that, while the main determinants of resistance may differ for the two pathogens, there could be an underlying common genetic basis. The exploration of regions physically close to the associated markers yielded 364 genes, of which 19 were predicted as putative disease resistance genes. This work presents the first simultaneous evaluation of two manifestations of Diaporthe/Phomopsis in sunflower, and undertakes a comprehensive GWA study by integrating PSC, PHR, and SHR data. The multiple regions identified, and their exploration to identify candidate genes, contribute not only to the understanding of the genetic basis of resistance, but also to the development of tools for assisted breeding.Instituto de BiotecnologíaFil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Filippi, Carla Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Corro Molas, Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Anguil. Agencia de Extensión Rural General Pico; ArgentinaFil: Dominguez, Matías. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino; ArgentinaFil: Colombo, Denis Nahuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Anguil; ArgentinaFil: Heinz, N. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; ArgentinaFil: Troglia, Carolina Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Maringolo, Carla Andrea. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Quiroz, Facundo Jose. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Alvarez, Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; ArgentinaFil: Lia, Veronica Viviana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Lia, Veronica Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Lia, Veronica Viviana. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; ArgentinaFil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; ArgentinaFil: Paniego, Norma Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaMDPI2022-12-26T10:46:01Z2022-12-26T10:46:01Z2022-12info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/13697https://www.mdpi.com/2073-4425/13/12/23572073-4425https://doi.org/10.3390/genes13122357Genes 13 (12) : 2357 (Diciembre 2022)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repograntAgreement/INTA/2019-PE-E6-I114-001/2019-PE-E6-I114-001/AR./Caracterización de la diversidad genética de plantas, animales y microorganismos mediante herramientas de genómica aplicada.info:eu-repograntAgreement/INTA/2019-PE-E6-I127-001/2019-PE-E6-I127-001/AR./Mejoramiento genético de soja, girasol y oleaginosas invernales en calidad y valor agregado, productividad, y estabilidad y plasticidad ante estreses bióticos y abióticosinfo:eu-repograntAgreement/INTA/2019-PD-E4-I090-001/2019-PD-E4-I090-001/AR./Análisis de patosistemas en cultivos agrícolas y especies forestales. Caracterización de sus componentesinfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)2025-09-04T09:49:41Zoai:localhost:20.500.12123/13697instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-04 09:49:41.413INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Genome-wide association studies in sunflower : towards sclerotinia sclerotiorum and diaporthe/phomopsis resistance breeding
title Genome-wide association studies in sunflower : towards sclerotinia sclerotiorum and diaporthe/phomopsis resistance breeding
spellingShingle Genome-wide association studies in sunflower : towards sclerotinia sclerotiorum and diaporthe/phomopsis resistance breeding
Filippi, Carla Valeria
Sunflowers
Diaporthe
Phomopsis
Genomes
Girasol
Helianthus annuus
Sclerotinia sclerotiorum
Diaporthe helianthi
Genomas
GWAS
title_short Genome-wide association studies in sunflower : towards sclerotinia sclerotiorum and diaporthe/phomopsis resistance breeding
title_full Genome-wide association studies in sunflower : towards sclerotinia sclerotiorum and diaporthe/phomopsis resistance breeding
title_fullStr Genome-wide association studies in sunflower : towards sclerotinia sclerotiorum and diaporthe/phomopsis resistance breeding
title_full_unstemmed Genome-wide association studies in sunflower : towards sclerotinia sclerotiorum and diaporthe/phomopsis resistance breeding
title_sort Genome-wide association studies in sunflower : towards sclerotinia sclerotiorum and diaporthe/phomopsis resistance breeding
dc.creator.none.fl_str_mv Filippi, Carla Valeria
Corro Molas, Andres Ezequiel
Dominguez, Matías
Colombo, Denis Nahuel
Heinz, Nicolás
Troglia, Carolina Beatriz
Maringolo, Carla Andrea
Quiroz, Facundo Jose
Alvarez, Daniel
Lia, Veronica Viviana
Paniego, Norma Beatriz
author Filippi, Carla Valeria
author_facet Filippi, Carla Valeria
Corro Molas, Andres Ezequiel
Dominguez, Matías
Colombo, Denis Nahuel
Heinz, Nicolás
Troglia, Carolina Beatriz
Maringolo, Carla Andrea
Quiroz, Facundo Jose
Alvarez, Daniel
Lia, Veronica Viviana
Paniego, Norma Beatriz
author_role author
author2 Corro Molas, Andres Ezequiel
Dominguez, Matías
Colombo, Denis Nahuel
Heinz, Nicolás
Troglia, Carolina Beatriz
Maringolo, Carla Andrea
Quiroz, Facundo Jose
Alvarez, Daniel
Lia, Veronica Viviana
Paniego, Norma Beatriz
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Sunflowers
Diaporthe
Phomopsis
Genomes
Girasol
Helianthus annuus
Sclerotinia sclerotiorum
Diaporthe helianthi
Genomas
GWAS
topic Sunflowers
Diaporthe
Phomopsis
Genomes
Girasol
Helianthus annuus
Sclerotinia sclerotiorum
Diaporthe helianthi
Genomas
GWAS
dc.description.none.fl_txt_mv Diseases caused by necrotrophic fungi, such as the cosmopolitan Sclerotinia sclerotiorum and the Diaporthe/Phomopsis complex, are among the most destructive diseases of sunflower worldwide. The lack of complete resistance combined with the inefficiency of chemical control makes assisted breeding the best strategy for disease control. In this work, we present an integrated genome-wide association (GWA) study investigating the response of a diverse panel of sunflower inbred lines to both pathogens. Phenotypic data for Sclerotinia head rot (SHR) consisted of five disease descriptors (disease incidence, DI; disease severity, DS; area under the disease progress curve for DI, AUDPCI, and DS, AUDPCS; and incubation period, IP). Two disease descriptors (DI and DS) were evaluated for two manifestations of Diaporthe/Phomopsis: Phomopsis stem canker (PSC) and Phomopsis head rot (PHR). In addition, a principal component (PC) analysis was used to derive transformed phenotypes as inputs to a univariateGWA (PC-GWA). Genotypic data comprised a panel of 4269 single nucleotide polymorphisms (SNP), generated via genotyping-by-sequencing. The GWA analysis revealed 24 unique marker–trait associations for SHR, 19 unique marker–trait associations for Diaporthe/Phomopsis diseases, and 7 markers associated with PC1 and PC2. No common markers were found for the response to the two pathogens. Nevertheless, epistatic interactions were identified between markers significantly associated with the response to S. sclerotiorum and Diaporthe/Phomopsis. This suggests that, while the main determinants of resistance may differ for the two pathogens, there could be an underlying common genetic basis. The exploration of regions physically close to the associated markers yielded 364 genes, of which 19 were predicted as putative disease resistance genes. This work presents the first simultaneous evaluation of two manifestations of Diaporthe/Phomopsis in sunflower, and undertakes a comprehensive GWA study by integrating PSC, PHR, and SHR data. The multiple regions identified, and their exploration to identify candidate genes, contribute not only to the understanding of the genetic basis of resistance, but also to the development of tools for assisted breeding.
Instituto de Biotecnología
Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Filippi, Carla Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Corro Molas, Andres. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Anguil. Agencia de Extensión Rural General Pico; Argentina
Fil: Dominguez, Matías. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino; Argentina
Fil: Colombo, Denis Nahuel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Anguil; Argentina
Fil: Heinz, N. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Troglia, Carolina Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina
Fil: Maringolo, Carla Andrea. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina
Fil: Quiroz, Facundo Jose. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina
Fil: Alvarez, Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Lia, Veronica Viviana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Lia, Veronica Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Lia, Veronica Viviana. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina
Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Agrobiotecnología y Biología Molecular; Argentina
Fil: Paniego, Norma Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
description Diseases caused by necrotrophic fungi, such as the cosmopolitan Sclerotinia sclerotiorum and the Diaporthe/Phomopsis complex, are among the most destructive diseases of sunflower worldwide. The lack of complete resistance combined with the inefficiency of chemical control makes assisted breeding the best strategy for disease control. In this work, we present an integrated genome-wide association (GWA) study investigating the response of a diverse panel of sunflower inbred lines to both pathogens. Phenotypic data for Sclerotinia head rot (SHR) consisted of five disease descriptors (disease incidence, DI; disease severity, DS; area under the disease progress curve for DI, AUDPCI, and DS, AUDPCS; and incubation period, IP). Two disease descriptors (DI and DS) were evaluated for two manifestations of Diaporthe/Phomopsis: Phomopsis stem canker (PSC) and Phomopsis head rot (PHR). In addition, a principal component (PC) analysis was used to derive transformed phenotypes as inputs to a univariateGWA (PC-GWA). Genotypic data comprised a panel of 4269 single nucleotide polymorphisms (SNP), generated via genotyping-by-sequencing. The GWA analysis revealed 24 unique marker–trait associations for SHR, 19 unique marker–trait associations for Diaporthe/Phomopsis diseases, and 7 markers associated with PC1 and PC2. No common markers were found for the response to the two pathogens. Nevertheless, epistatic interactions were identified between markers significantly associated with the response to S. sclerotiorum and Diaporthe/Phomopsis. This suggests that, while the main determinants of resistance may differ for the two pathogens, there could be an underlying common genetic basis. The exploration of regions physically close to the associated markers yielded 364 genes, of which 19 were predicted as putative disease resistance genes. This work presents the first simultaneous evaluation of two manifestations of Diaporthe/Phomopsis in sunflower, and undertakes a comprehensive GWA study by integrating PSC, PHR, and SHR data. The multiple regions identified, and their exploration to identify candidate genes, contribute not only to the understanding of the genetic basis of resistance, but also to the development of tools for assisted breeding.
publishDate 2022
dc.date.none.fl_str_mv 2022-12-26T10:46:01Z
2022-12-26T10:46:01Z
2022-12
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/13697
https://www.mdpi.com/2073-4425/13/12/2357
2073-4425
https://doi.org/10.3390/genes13122357
url http://hdl.handle.net/20.500.12123/13697
https://www.mdpi.com/2073-4425/13/12/2357
https://doi.org/10.3390/genes13122357
identifier_str_mv 2073-4425
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repograntAgreement/INTA/2019-PE-E6-I114-001/2019-PE-E6-I114-001/AR./Caracterización de la diversidad genética de plantas, animales y microorganismos mediante herramientas de genómica aplicada.
info:eu-repograntAgreement/INTA/2019-PE-E6-I127-001/2019-PE-E6-I127-001/AR./Mejoramiento genético de soja, girasol y oleaginosas invernales en calidad y valor agregado, productividad, y estabilidad y plasticidad ante estreses bióticos y abióticos
info:eu-repograntAgreement/INTA/2019-PD-E4-I090-001/2019-PD-E4-I090-001/AR./Análisis de patosistemas en cultivos agrícolas y especies forestales. Caracterización de sus componentes
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv Genes 13 (12) : 2357 (Diciembre 2022)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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