Efficient genomics-based ‘end-to-end’ selective tree breeding framework

Autores
El-Kassaby, Yousry A.; Cappa, Eduardo Pablo; Chen, Charles; Ratcliffe, Blaise; Porth, Ilga M.
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Since their initiation in the 1950s, worldwide selective tree breeding programs followed the recurrent selection scheme of repeated cycles of selection, breeding (mating), and testing phases and essentially remained unchanged to accelerate this process or address environmental contingencies and concerns. Here, we introduce an “end-to-end” selective tree breeding framework that: (1) leverages strategically preselected GWAS-based sequence data capturing trait architecture information, (2) generates unprecedented resolution of genealogical relationships among tested individuals, and (3) leads to the elimination of the breeding phase through the utilization of readily available wind-pollinated (OP) families. Individuals’ breeding values generated from multi-trait multi-site analysis were also used in an optimum contribution selection protocol to effectively manage genetic gain/co-ancestry trade-offs and traits’ correlated response to selection. The proof-of-concept study involved a 40-year-old spruce OP testing population growing on three sites in British Columbia, Canada, clearly demonstrating our method’s superiority in capturing most of the available genetic gains in a substantially reduced timeline relative to the traditional approach. The proposed framework is expected to increase the efficiency of existing selective breeding programs, accelerate the start of new programs for ecologically and environmentally important tree species, and address climate-change caused biotic and abiotic stress concerns more effectively.
Instituto de Recursos Biológicos
Fil: El-Kassaby, Yousry A. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá
Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina
Fil: Chen, Charles. Oklahoma State University. Department of Biochemistry and Molecular Biology; Estados Unidos
Fil: Rateliffe, Blaise. University of British Columbia, Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá
Fil: Porth, Ilga. Université Laval Québec. Faculté de Foresterie, de Géographie et Géomatique. Départment des Sciences du Bois et de la Forêt; Canadá
Fuente
Heredity 132 : 98-105. (2024)
Materia
Fitomejoramiento
Plant Breeding
Genomics
Genómica
Mejoramiento Selectivo de Arboles
Selective Tree Breeding
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
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spelling Efficient genomics-based ‘end-to-end’ selective tree breeding frameworkEl-Kassaby, Yousry A.Cappa, Eduardo PabloChen, CharlesRatcliffe, BlaisePorth, Ilga M.FitomejoramientoPlant BreedingGenomicsGenómicaMejoramiento Selectivo de ArbolesSelective Tree BreedingSince their initiation in the 1950s, worldwide selective tree breeding programs followed the recurrent selection scheme of repeated cycles of selection, breeding (mating), and testing phases and essentially remained unchanged to accelerate this process or address environmental contingencies and concerns. Here, we introduce an “end-to-end” selective tree breeding framework that: (1) leverages strategically preselected GWAS-based sequence data capturing trait architecture information, (2) generates unprecedented resolution of genealogical relationships among tested individuals, and (3) leads to the elimination of the breeding phase through the utilization of readily available wind-pollinated (OP) families. Individuals’ breeding values generated from multi-trait multi-site analysis were also used in an optimum contribution selection protocol to effectively manage genetic gain/co-ancestry trade-offs and traits’ correlated response to selection. The proof-of-concept study involved a 40-year-old spruce OP testing population growing on three sites in British Columbia, Canada, clearly demonstrating our method’s superiority in capturing most of the available genetic gains in a substantially reduced timeline relative to the traditional approach. The proposed framework is expected to increase the efficiency of existing selective breeding programs, accelerate the start of new programs for ecologically and environmentally important tree species, and address climate-change caused biotic and abiotic stress concerns more effectively.Instituto de Recursos BiológicosFil: El-Kassaby, Yousry A. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáFil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; ArgentinaFil: Chen, Charles. Oklahoma State University. Department of Biochemistry and Molecular Biology; Estados UnidosFil: Rateliffe, Blaise. University of British Columbia, Faculty of Forestry. Department of Forest and Conservation Sciences; CanadáFil: Porth, Ilga. Université Laval Québec. Faculté de Foresterie, de Géographie et Géomatique. Départment des Sciences du Bois et de la Forêt; CanadáSpringer Nature2024-03-27T18:08:58Z2024-03-27T18:08:58Z2024-01-03info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/17251https://www.nature.com/articles/s41437-023-00667-w1365-25400018-067Xhttps://doi.org/10.1038/s41437-023-00667-wHeredity 132 : 98-105. (2024)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo: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)2025-10-23T11:18:46Zoai:localhost:20.500.12123/17251instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-10-23 11:18:47.011INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Efficient genomics-based ‘end-to-end’ selective tree breeding framework
title Efficient genomics-based ‘end-to-end’ selective tree breeding framework
spellingShingle Efficient genomics-based ‘end-to-end’ selective tree breeding framework
El-Kassaby, Yousry A.
Fitomejoramiento
Plant Breeding
Genomics
Genómica
Mejoramiento Selectivo de Arboles
Selective Tree Breeding
title_short Efficient genomics-based ‘end-to-end’ selective tree breeding framework
title_full Efficient genomics-based ‘end-to-end’ selective tree breeding framework
title_fullStr Efficient genomics-based ‘end-to-end’ selective tree breeding framework
title_full_unstemmed Efficient genomics-based ‘end-to-end’ selective tree breeding framework
title_sort Efficient genomics-based ‘end-to-end’ selective tree breeding framework
dc.creator.none.fl_str_mv El-Kassaby, Yousry A.
Cappa, Eduardo Pablo
Chen, Charles
Ratcliffe, Blaise
Porth, Ilga M.
author El-Kassaby, Yousry A.
author_facet El-Kassaby, Yousry A.
Cappa, Eduardo Pablo
Chen, Charles
Ratcliffe, Blaise
Porth, Ilga M.
author_role author
author2 Cappa, Eduardo Pablo
Chen, Charles
Ratcliffe, Blaise
Porth, Ilga M.
author2_role author
author
author
author
dc.subject.none.fl_str_mv Fitomejoramiento
Plant Breeding
Genomics
Genómica
Mejoramiento Selectivo de Arboles
Selective Tree Breeding
topic Fitomejoramiento
Plant Breeding
Genomics
Genómica
Mejoramiento Selectivo de Arboles
Selective Tree Breeding
dc.description.none.fl_txt_mv Since their initiation in the 1950s, worldwide selective tree breeding programs followed the recurrent selection scheme of repeated cycles of selection, breeding (mating), and testing phases and essentially remained unchanged to accelerate this process or address environmental contingencies and concerns. Here, we introduce an “end-to-end” selective tree breeding framework that: (1) leverages strategically preselected GWAS-based sequence data capturing trait architecture information, (2) generates unprecedented resolution of genealogical relationships among tested individuals, and (3) leads to the elimination of the breeding phase through the utilization of readily available wind-pollinated (OP) families. Individuals’ breeding values generated from multi-trait multi-site analysis were also used in an optimum contribution selection protocol to effectively manage genetic gain/co-ancestry trade-offs and traits’ correlated response to selection. The proof-of-concept study involved a 40-year-old spruce OP testing population growing on three sites in British Columbia, Canada, clearly demonstrating our method’s superiority in capturing most of the available genetic gains in a substantially reduced timeline relative to the traditional approach. The proposed framework is expected to increase the efficiency of existing selective breeding programs, accelerate the start of new programs for ecologically and environmentally important tree species, and address climate-change caused biotic and abiotic stress concerns more effectively.
Instituto de Recursos Biológicos
Fil: El-Kassaby, Yousry A. University of British Columbia. Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá
Fil: Cappa, Eduardo Pablo. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina
Fil: Chen, Charles. Oklahoma State University. Department of Biochemistry and Molecular Biology; Estados Unidos
Fil: Rateliffe, Blaise. University of British Columbia, Faculty of Forestry. Department of Forest and Conservation Sciences; Canadá
Fil: Porth, Ilga. Université Laval Québec. Faculté de Foresterie, de Géographie et Géomatique. Départment des Sciences du Bois et de la Forêt; Canadá
description Since their initiation in the 1950s, worldwide selective tree breeding programs followed the recurrent selection scheme of repeated cycles of selection, breeding (mating), and testing phases and essentially remained unchanged to accelerate this process or address environmental contingencies and concerns. Here, we introduce an “end-to-end” selective tree breeding framework that: (1) leverages strategically preselected GWAS-based sequence data capturing trait architecture information, (2) generates unprecedented resolution of genealogical relationships among tested individuals, and (3) leads to the elimination of the breeding phase through the utilization of readily available wind-pollinated (OP) families. Individuals’ breeding values generated from multi-trait multi-site analysis were also used in an optimum contribution selection protocol to effectively manage genetic gain/co-ancestry trade-offs and traits’ correlated response to selection. The proof-of-concept study involved a 40-year-old spruce OP testing population growing on three sites in British Columbia, Canada, clearly demonstrating our method’s superiority in capturing most of the available genetic gains in a substantially reduced timeline relative to the traditional approach. The proposed framework is expected to increase the efficiency of existing selective breeding programs, accelerate the start of new programs for ecologically and environmentally important tree species, and address climate-change caused biotic and abiotic stress concerns more effectively.
publishDate 2024
dc.date.none.fl_str_mv 2024-03-27T18:08:58Z
2024-03-27T18:08:58Z
2024-01-03
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/20.500.12123/17251
https://www.nature.com/articles/s41437-023-00667-w
1365-2540
0018-067X
https://doi.org/10.1038/s41437-023-00667-w
url http://hdl.handle.net/20.500.12123/17251
https://www.nature.com/articles/s41437-023-00667-w
https://doi.org/10.1038/s41437-023-00667-w
identifier_str_mv 1365-2540
0018-067X
dc.language.none.fl_str_mv eng
language eng
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 Springer Nature
publisher.none.fl_str_mv Springer Nature
dc.source.none.fl_str_mv Heredity 132 : 98-105. (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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score 12.982451

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