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
.jpg)
- Institución
- Instituto Nacional de Tecnología Agropecuaria
- OAI Identificador
- oai:localhost:20.500.12123/18691
Ver los metadatos del registro completo
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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)2025-09-29T13:46:40Zoai: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:l2025-09-29 13:46:40.983INTA 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) |
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openAccess |
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http://creativecommons.org/licenses/by-nc-sa/4.0/ Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) |
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application/pdf |
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American Peanut Research and Education Society |
| publisher.none.fl_str_mv |
American Peanut Research and Education Society |
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Peanut Science 51 (1) : 59-65. (2024) reponame:INTA Digital (INTA) instname:Instituto Nacional de Tecnología Agropecuaria |
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