Discovery of a resistance gene cluster associated with smut resistance in peanut

Autores
Chamberlin, Kelly D.; Bennett, Rebecca S.; Baldessari, Jorge Javier; De La Barrera, Guillermo; Cordes, Guillermo; Grandon, Nancy Gabriela; Mamani, Eva Maria Celia; Rodriguez, Ana Valeria; Morchetti, Sergio; Holbrook, Corley C.; Ozias-Akins, Peggy; Ye, Chu; Tallury, Shyam P.; Clevenger, Josh; Korani, W.; Scheffler, Brian; Youngblood, Ramey Callahan; Simpson, Sheron
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Peanut smut, caused by Thecaphora frezzii Carranza & J.C. Lindq., is an emerging threat for the global peanut industry. The disease’s destructive potential can be exemplified by pod incidence values as high as 70% and yield losses reaching 30%. Because fungicides have shown moderate but highly variable levels of control levels, development and deployment of smut resistant cultivars are the best strategies for disease management. Screening for smut-resistant germplasm requires years of field trials and is currently the only option for breeders because genetic markers for resistance have not yet been developed. The objectives of this study were to perform whole genome sequencing (WGS) on populations developed for smut resistance mapping and subsequently fine map discovered QTL associated with smut resistance. An expedited strategy was employed by phenotyping in the F3 generation. We phenotyped 200 families with 3 plants per family for smut resistance in infested fields during the 2019/2020 season in General Deheza (32°45′23″S 63°47′20″W), Argentina. Each individual was sequenced using iGenomXRipTide library preparation and Illumina NovaSeq sequencing to yield approximately 1 times genome coverage. Analysis of the phenotype and genotype data using Khufu resulted in the identification of a single major smut resistance QTL on chromosome 12 (B02). Chromosome level genome sequences were assembled for the resistant parent (Ascasubi) and susceptible parent (Granoleico) using PacBio HIFI sequencing. A validation population was sequenced using Khufu to validate the QTL region and analysis confirmed the major locus on chromosome 12. The identified variation will be used to develop smut resistant varieties quickly using molecular assisted breeding strategies.
EEA Manfredi
Fil: Chamberlin, K.D. USDA. Agricultural Research Service. Wheat, Peanut and Other Field Crops Research Unit; Estados Unidos
Fil: Bennetti, Rebecca S. USDA-ARS, Peanut and Small Grains Research Unit, Stillwater, Oklahoma
Fil: Baldessari, Jorge Javier. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: De la Barrera, Guillermo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Cordes, Guillermo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Grandon, Nancy Gabriela. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Mamani, Eva María Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Rodriguez, Ana Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Morchetti, Sergio. Aceitera General Deheza; Argentina
Fil: Holbrook, C.C. USDA-ARS. Crop Genetics and Breeding Research Unit; Estados Unidos
Fil: Ozias-Akins, P. University of Georgia. Institute of Plant Breeding, Genetics, and Genomics. National Environmentally Sound Production Agriculture Laboratory; Estados Unidos
Fil: Chu, Y. University of Georgia. Institute of Plant Breeding, Genetics, and Genomics. National Environmentally Sound Production Agriculture Laboratory; Estados Unidos
Fil: Tallury, S. P. USDA-ARS. Plant Genetic Resources Conservation Unit; Estados Unidos
Fil: Clevenger, J. HudsonAlpha Institute for Biotechnology; Estados Unidos
Fil: Korani, W. HudsonAlpha Institute for Biotechnology; Estados Unidos
Fil: Scheffler, B. USDA-ARS. Genomics and Bioinformatics Research Unit; Estados Unidos
Fil. Youngblood, R. USDA-ARS. Genomics and Bioinformatics Research Unit; Estados Unidos
Fil: Simpson, S. USDA-ARS. Genomics and Bioinformatics Research Unit; Estados Unidos
Fuente
Peanut Science 51 (1) : 59-65. (2024)
Materia
Arachis hypogaea
Cacahuete
Carbón
Groundnuts
Smuts
Plant Diseases
Enfermedades de las Plantas
Maní
Carbón del Maní
Peanuts
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:20.500.12123/18691

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network_name_str INTA Digital (INTA)
spelling Discovery of a resistance gene cluster associated with smut resistance in peanutChamberlin, Kelly D.Bennett, Rebecca S.Baldessari, Jorge JavierDe La Barrera, GuillermoCordes, GuillermoGrandon, Nancy GabrielaMamani, Eva Maria CeliaRodriguez, Ana ValeriaMorchetti, SergioHolbrook, Corley C.Ozias-Akins, PeggyYe, ChuTallury, Shyam P.Clevenger, JoshKorani, W.Scheffler, BrianYoungblood, Ramey CallahanSimpson, SheronArachis hypogaeaCacahueteCarbónGroundnutsSmutsPlant DiseasesEnfermedades de las PlantasManíCarbón del ManíPeanutsPeanut smut, caused by Thecaphora frezzii Carranza & J.C. Lindq., is an emerging threat for the global peanut industry. The disease’s destructive potential can be exemplified by pod incidence values as high as 70% and yield losses reaching 30%. Because fungicides have shown moderate but highly variable levels of control levels, development and deployment of smut resistant cultivars are the best strategies for disease management. Screening for smut-resistant germplasm requires years of field trials and is currently the only option for breeders because genetic markers for resistance have not yet been developed. The objectives of this study were to perform whole genome sequencing (WGS) on populations developed for smut resistance mapping and subsequently fine map discovered QTL associated with smut resistance. An expedited strategy was employed by phenotyping in the F3 generation. We phenotyped 200 families with 3 plants per family for smut resistance in infested fields during the 2019/2020 season in General Deheza (32°45′23″S 63°47′20″W), Argentina. Each individual was sequenced using iGenomXRipTide library preparation and Illumina NovaSeq sequencing to yield approximately 1 times genome coverage. Analysis of the phenotype and genotype data using Khufu resulted in the identification of a single major smut resistance QTL on chromosome 12 (B02). Chromosome level genome sequences were assembled for the resistant parent (Ascasubi) and susceptible parent (Granoleico) using PacBio HIFI sequencing. A validation population was sequenced using Khufu to validate the QTL region and analysis confirmed the major locus on chromosome 12. The identified variation will be used to develop smut resistant varieties quickly using molecular assisted breeding strategies.EEA ManfrediFil: Chamberlin, K.D. USDA. Agricultural Research Service. Wheat, Peanut and Other Field Crops Research Unit; Estados UnidosFil: Bennetti, Rebecca S. USDA-ARS, Peanut and Small Grains Research Unit, Stillwater, OklahomaFil: Baldessari, Jorge Javier. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; ArgentinaFil: De la Barrera, Guillermo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; ArgentinaFil: Cordes, Guillermo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; ArgentinaFil: Grandon, Nancy Gabriela. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; ArgentinaFil: Mamani, Eva María Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; ArgentinaFil: Rodriguez, Ana Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; ArgentinaFil: Morchetti, Sergio. Aceitera General Deheza; ArgentinaFil: Holbrook, C.C. USDA-ARS. Crop Genetics and Breeding Research Unit; Estados UnidosFil: Ozias-Akins, P. University of Georgia. Institute of Plant Breeding, Genetics, and Genomics. National Environmentally Sound Production Agriculture Laboratory; Estados UnidosFil: Chu, Y. University of Georgia. Institute of Plant Breeding, Genetics, and Genomics. National Environmentally Sound Production Agriculture Laboratory; Estados UnidosFil: Tallury, S. P. USDA-ARS. Plant Genetic Resources Conservation Unit; Estados UnidosFil: Clevenger, J. HudsonAlpha Institute for Biotechnology; Estados UnidosFil: Korani, W. HudsonAlpha Institute for Biotechnology; Estados UnidosFil: Scheffler, B. USDA-ARS. Genomics and Bioinformatics Research Unit; Estados UnidosFil. Youngblood, R. USDA-ARS. Genomics and Bioinformatics Research Unit; Estados UnidosFil: Simpson, S. USDA-ARS. Genomics and Bioinformatics Research Unit; Estados UnidosAmerican Peanut Research and Education Society2024-07-29T10:33:58Z2024-07-29T10:33:58Z2024-06-14info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/18691https://peanutscience.com/article/id/1615/Chamberlin, K. y Bennett, R. y Baldessari, J. y De la Barrera, G. y Cordes, GG y Grandon, NG y Mamani, EM y Rodriquez, A. y Morchetti, S. y Holbrook, CC y Ozias-Akins, P. y Chu, Y. y Tallury, S. y Clevenger, J. y Korani, W. y Scheffler, B. y Youngblood, RC y Simpson, S. (2024) “Descubrimiento de un grupo de genes de resistencia asociado con la resistencia al carbón en el maní”, Peanut Science 51(1), págs. 59-65. doi: https://doi.org/10.3146/0095-3679-51-PS23-6https://doi.org/10.3146/0095-3679-51-PS23-6Peanut Science 51 (1) : 59-65. (2024)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repograntAgreement/INTA/2023-PD-L01-I087, Caracterización de la diversidad genética de plantas, animales y microorganismos mediante herramientas de genómica aplicada.info:eu-repograntAgreement/INTA/2023-PD-L01-I071, Mejoramiento genético de los Cultivos Industriales y estrategias alternativas para la obtención de biotipos adaptados a los nuevos escenarios y al cambio climáticoinfo: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)2025-09-04T09:50:31Zoai:localhost:20.500.12123/18691instacron: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 09:50:32.101INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Discovery of a resistance gene cluster associated with smut resistance in peanut
title Discovery of a resistance gene cluster associated with smut resistance in peanut
spellingShingle Discovery of a resistance gene cluster associated with smut resistance in peanut
Chamberlin, Kelly D.
Arachis hypogaea
Cacahuete
Carbón
Groundnuts
Smuts
Plant Diseases
Enfermedades de las Plantas
Maní
Carbón del Maní
Peanuts
title_short Discovery of a resistance gene cluster associated with smut resistance in peanut
title_full Discovery of a resistance gene cluster associated with smut resistance in peanut
title_fullStr Discovery of a resistance gene cluster associated with smut resistance in peanut
title_full_unstemmed Discovery of a resistance gene cluster associated with smut resistance in peanut
title_sort Discovery of a resistance gene cluster associated with smut resistance in peanut
dc.creator.none.fl_str_mv Chamberlin, Kelly D.
Bennett, Rebecca S.
Baldessari, Jorge Javier
De La Barrera, Guillermo
Cordes, Guillermo
Grandon, Nancy Gabriela
Mamani, Eva Maria Celia
Rodriguez, Ana Valeria
Morchetti, Sergio
Holbrook, Corley C.
Ozias-Akins, Peggy
Ye, Chu
Tallury, Shyam P.
Clevenger, Josh
Korani, W.
Scheffler, Brian
Youngblood, Ramey Callahan
Simpson, Sheron
author Chamberlin, Kelly D.
author_facet Chamberlin, Kelly D.
Bennett, Rebecca S.
Baldessari, Jorge Javier
De La Barrera, Guillermo
Cordes, Guillermo
Grandon, Nancy Gabriela
Mamani, Eva Maria Celia
Rodriguez, Ana Valeria
Morchetti, Sergio
Holbrook, Corley C.
Ozias-Akins, Peggy
Ye, Chu
Tallury, Shyam P.
Clevenger, Josh
Korani, W.
Scheffler, Brian
Youngblood, Ramey Callahan
Simpson, Sheron
author_role author
author2 Bennett, Rebecca S.
Baldessari, Jorge Javier
De La Barrera, Guillermo
Cordes, Guillermo
Grandon, Nancy Gabriela
Mamani, Eva Maria Celia
Rodriguez, Ana Valeria
Morchetti, Sergio
Holbrook, Corley C.
Ozias-Akins, Peggy
Ye, Chu
Tallury, Shyam P.
Clevenger, Josh
Korani, W.
Scheffler, Brian
Youngblood, Ramey Callahan
Simpson, Sheron
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Arachis hypogaea
Cacahuete
Carbón
Groundnuts
Smuts
Plant Diseases
Enfermedades de las Plantas
Maní
Carbón del Maní
Peanuts
topic Arachis hypogaea
Cacahuete
Carbón
Groundnuts
Smuts
Plant Diseases
Enfermedades de las Plantas
Maní
Carbón del Maní
Peanuts
dc.description.none.fl_txt_mv Peanut smut, caused by Thecaphora frezzii Carranza & J.C. Lindq., is an emerging threat for the global peanut industry. The disease’s destructive potential can be exemplified by pod incidence values as high as 70% and yield losses reaching 30%. Because fungicides have shown moderate but highly variable levels of control levels, development and deployment of smut resistant cultivars are the best strategies for disease management. Screening for smut-resistant germplasm requires years of field trials and is currently the only option for breeders because genetic markers for resistance have not yet been developed. The objectives of this study were to perform whole genome sequencing (WGS) on populations developed for smut resistance mapping and subsequently fine map discovered QTL associated with smut resistance. An expedited strategy was employed by phenotyping in the F3 generation. We phenotyped 200 families with 3 plants per family for smut resistance in infested fields during the 2019/2020 season in General Deheza (32°45′23″S 63°47′20″W), Argentina. Each individual was sequenced using iGenomXRipTide library preparation and Illumina NovaSeq sequencing to yield approximately 1 times genome coverage. Analysis of the phenotype and genotype data using Khufu resulted in the identification of a single major smut resistance QTL on chromosome 12 (B02). Chromosome level genome sequences were assembled for the resistant parent (Ascasubi) and susceptible parent (Granoleico) using PacBio HIFI sequencing. A validation population was sequenced using Khufu to validate the QTL region and analysis confirmed the major locus on chromosome 12. The identified variation will be used to develop smut resistant varieties quickly using molecular assisted breeding strategies.
EEA Manfredi
Fil: Chamberlin, K.D. USDA. Agricultural Research Service. Wheat, Peanut and Other Field Crops Research Unit; Estados Unidos
Fil: Bennetti, Rebecca S. USDA-ARS, Peanut and Small Grains Research Unit, Stillwater, Oklahoma
Fil: Baldessari, Jorge Javier. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: De la Barrera, Guillermo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Cordes, Guillermo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Grandon, Nancy Gabriela. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Mamani, Eva María Cecilia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Rodriguez, Ana Valeria. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina
Fil: Morchetti, Sergio. Aceitera General Deheza; Argentina
Fil: Holbrook, C.C. USDA-ARS. Crop Genetics and Breeding Research Unit; Estados Unidos
Fil: Ozias-Akins, P. University of Georgia. Institute of Plant Breeding, Genetics, and Genomics. National Environmentally Sound Production Agriculture Laboratory; Estados Unidos
Fil: Chu, Y. University of Georgia. Institute of Plant Breeding, Genetics, and Genomics. National Environmentally Sound Production Agriculture Laboratory; Estados Unidos
Fil: Tallury, S. P. USDA-ARS. Plant Genetic Resources Conservation Unit; Estados Unidos
Fil: Clevenger, J. HudsonAlpha Institute for Biotechnology; Estados Unidos
Fil: Korani, W. HudsonAlpha Institute for Biotechnology; Estados Unidos
Fil: Scheffler, B. USDA-ARS. Genomics and Bioinformatics Research Unit; Estados Unidos
Fil. Youngblood, R. USDA-ARS. Genomics and Bioinformatics Research Unit; Estados Unidos
Fil: Simpson, S. USDA-ARS. Genomics and Bioinformatics Research Unit; Estados Unidos
description Peanut smut, caused by Thecaphora frezzii Carranza & J.C. Lindq., is an emerging threat for the global peanut industry. The disease’s destructive potential can be exemplified by pod incidence values as high as 70% and yield losses reaching 30%. Because fungicides have shown moderate but highly variable levels of control levels, development and deployment of smut resistant cultivars are the best strategies for disease management. Screening for smut-resistant germplasm requires years of field trials and is currently the only option for breeders because genetic markers for resistance have not yet been developed. The objectives of this study were to perform whole genome sequencing (WGS) on populations developed for smut resistance mapping and subsequently fine map discovered QTL associated with smut resistance. An expedited strategy was employed by phenotyping in the F3 generation. We phenotyped 200 families with 3 plants per family for smut resistance in infested fields during the 2019/2020 season in General Deheza (32°45′23″S 63°47′20″W), Argentina. Each individual was sequenced using iGenomXRipTide library preparation and Illumina NovaSeq sequencing to yield approximately 1 times genome coverage. Analysis of the phenotype and genotype data using Khufu resulted in the identification of a single major smut resistance QTL on chromosome 12 (B02). Chromosome level genome sequences were assembled for the resistant parent (Ascasubi) and susceptible parent (Granoleico) using PacBio HIFI sequencing. A validation population was sequenced using Khufu to validate the QTL region and analysis confirmed the major locus on chromosome 12. The identified variation will be used to develop smut resistant varieties quickly using molecular assisted breeding strategies.
publishDate 2024
dc.date.none.fl_str_mv 2024-07-29T10:33:58Z
2024-07-29T10:33:58Z
2024-06-14
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/20.500.12123/18691
https://peanutscience.com/article/id/1615/
Chamberlin, K. y Bennett, R. y Baldessari, J. y De la Barrera, G. y Cordes, GG y Grandon, NG y Mamani, EM y Rodriquez, A. y Morchetti, S. y Holbrook, CC y Ozias-Akins, P. y Chu, Y. y Tallury, S. y Clevenger, J. y Korani, W. y Scheffler, B. y Youngblood, RC y Simpson, S. (2024) “Descubrimiento de un grupo de genes de resistencia asociado con la resistencia al carbón en el maní”, Peanut Science 51(1), págs. 59-65. doi: https://doi.org/10.3146/0095-3679-51-PS23-6
https://doi.org/10.3146/0095-3679-51-PS23-6
url http://hdl.handle.net/20.500.12123/18691
https://peanutscience.com/article/id/1615/
https://doi.org/10.3146/0095-3679-51-PS23-6
identifier_str_mv Chamberlin, K. y Bennett, R. y Baldessari, J. y De la Barrera, G. y Cordes, GG y Grandon, NG y Mamani, EM y Rodriquez, A. y Morchetti, S. y Holbrook, CC y Ozias-Akins, P. y Chu, Y. y Tallury, S. y Clevenger, J. y Korani, W. y Scheffler, B. y Youngblood, RC y Simpson, S. (2024) “Descubrimiento de un grupo de genes de resistencia asociado con la resistencia al carbón en el maní”, Peanut Science 51(1), págs. 59-65. doi: https://doi.org/10.3146/0095-3679-51-PS23-6
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repograntAgreement/INTA/2023-PD-L01-I087, Caracterización de la diversidad genética de plantas, animales y microorganismos mediante herramientas de genómica aplicada.
info:eu-repograntAgreement/INTA/2023-PD-L01-I071, Mejoramiento genético de los Cultivos Industriales y estrategias alternativas para la obtención de biotipos adaptados a los nuevos escenarios y al cambio climático
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 American Peanut Research and Education Society
publisher.none.fl_str_mv American Peanut Research and Education Society
dc.source.none.fl_str_mv Peanut Science 51 (1) : 59-65. (2024)
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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