Genomic prediction for broad and specific adaptation in sorghum accommodating differential variances of SNP effects

Autores
Velazco, Julio Gabriel; Jordan, David R.; Hunt, Colleen H.; Mace, Emma S.; van Eeuwijk, Fred A.
Año de publicación
2020
Idioma
inglés
Tipo de recurso
artículo
Estado
versión aceptada
Descripción
This paper reports a first study exploring genomic prediction for adaptation of sorghum [Sorghum bicolor (L.) Moench] to drought‐stress (D‐ET) and non‐stress (W‐ET) environment types. The objective was to evaluate the impact of both modeling genotype‐by‐environment interaction (G × E) and accounting for heterogeneous variances of marker effects on genomic prediction of parental breeding values for grain yield within and across environment types (ET). For this aim, different genetic covariance structures and different weights for individual markers were investigated in BLUP‐based prediction models. The BLUP models used a kinship matrix combining pedigree and genomic information, termed K‐BLUP. The dataset comprised testcross yield performances under D‐ET and W‐ET as well as pedigree and genomic data. In general, modeling G × E increased predictive ability and reduced empirical bias of genomic predictions for broad adaptation across both ETs compared to models that ignored G × E by fitting a main genetic effect only. Genomic predictions for specific adaptation to D‐ET or to W‐ET were also improved by K‐BLUP models that explicitly accommodated G × E and used data from both ETs, relative to prediction models that used data from the targeted ET exclusively or models that used all the data but assumed no G × E. Allowing for heterogeneous marker variances through weighted K‐BLUP produced clear increments (between 43% and 72%) in predictive ability of genomic prediction for grain yield in all adaptation scenarios. We conclude that G × E as well as locus‐specific genetic variances should be accommodated in genomic prediction models to improve adaptability of sorghum to variable environmental conditions.
EEA Pergamino
Fil: Velazco, Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino. Sección Forrajeras; Argentina. Wageningen University and Research . Biometris – Mathematical and Statistical Methods; Holanda
Fil: Jordan, David R. The University of Queensland. Hermitage Research Facility. Queensland Alliance for Agriculture and Food Innovation; Australia
Fil: Hunt, Colleen H. The University of Queensland. Hermitage Research Facility. Queensland Alliance for Agriculture and Food Innovation; Australia. Hermitage Research Facility. Department of Agriculture and Fisheries; Australia
Fil: Mace, Emma S. The University of Queensland. Hermitage Research Facility. Queensland Alliance for Agriculture and Food Innovation; Australia. Hermitage Research Facility. Department of Agriculture and Fisheries; Australia
Fil: Eeuwijk, Fred A. van. Wageningen University and Research . Biometris – Mathematical and Statistical Methods; Holanda
Fuente
Crop Science 60 (3) : 1-33 (May -June 2020)
Materia
Sorgos
Mejora Genética
Fitomejoramiento
Forrajes
Sorghum Grain
Genetic Gain
Plant Breeding
Forage
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/7601

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oai_identifier_str oai:localhost:20.500.12123/7601
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network_name_str INTA Digital (INTA)
spelling Genomic prediction for broad and specific adaptation in sorghum accommodating differential variances of SNP effectsVelazco, Julio GabrielJordan, David R.Hunt, Colleen H.Mace, Emma S.van Eeuwijk, Fred A.SorgosMejora GenéticaFitomejoramientoForrajesSorghum GrainGenetic GainPlant BreedingForageThis paper reports a first study exploring genomic prediction for adaptation of sorghum [Sorghum bicolor (L.) Moench] to drought‐stress (D‐ET) and non‐stress (W‐ET) environment types. The objective was to evaluate the impact of both modeling genotype‐by‐environment interaction (G × E) and accounting for heterogeneous variances of marker effects on genomic prediction of parental breeding values for grain yield within and across environment types (ET). For this aim, different genetic covariance structures and different weights for individual markers were investigated in BLUP‐based prediction models. The BLUP models used a kinship matrix combining pedigree and genomic information, termed K‐BLUP. The dataset comprised testcross yield performances under D‐ET and W‐ET as well as pedigree and genomic data. In general, modeling G × E increased predictive ability and reduced empirical bias of genomic predictions for broad adaptation across both ETs compared to models that ignored G × E by fitting a main genetic effect only. Genomic predictions for specific adaptation to D‐ET or to W‐ET were also improved by K‐BLUP models that explicitly accommodated G × E and used data from both ETs, relative to prediction models that used data from the targeted ET exclusively or models that used all the data but assumed no G × E. Allowing for heterogeneous marker variances through weighted K‐BLUP produced clear increments (between 43% and 72%) in predictive ability of genomic prediction for grain yield in all adaptation scenarios. We conclude that G × E as well as locus‐specific genetic variances should be accommodated in genomic prediction models to improve adaptability of sorghum to variable environmental conditions.EEA PergaminoFil: Velazco, Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino. Sección Forrajeras; Argentina. Wageningen University and Research . Biometris – Mathematical and Statistical Methods; HolandaFil: Jordan, David R. The University of Queensland. Hermitage Research Facility. Queensland Alliance for Agriculture and Food Innovation; AustraliaFil: Hunt, Colleen H. The University of Queensland. Hermitage Research Facility. Queensland Alliance for Agriculture and Food Innovation; Australia. Hermitage Research Facility. Department of Agriculture and Fisheries; AustraliaFil: Mace, Emma S. The University of Queensland. Hermitage Research Facility. Queensland Alliance for Agriculture and Food Innovation; Australia. Hermitage Research Facility. Department of Agriculture and Fisheries; AustraliaFil: Eeuwijk, Fred A. van. Wageningen University and Research . Biometris – Mathematical and Statistical Methods; HolandaAmerican Society of Agronomy2020-07-23T13:29:25Z2020-07-23T13:29:25Z2020-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/7601https://acsess.onlinelibrary.wiley.com/doi/abs/10.1002/csc2.202211435-0653 (online)https://doi.org/10.1002/csc2.20221Crop Science 60 (3) : 1-33 (May -June 2020)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccess2025-09-29T13:44:59Zoai:localhost:20.500.12123/7601instacron: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 13:44:59.404INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Genomic prediction for broad and specific adaptation in sorghum accommodating differential variances of SNP effects
title Genomic prediction for broad and specific adaptation in sorghum accommodating differential variances of SNP effects
spellingShingle Genomic prediction for broad and specific adaptation in sorghum accommodating differential variances of SNP effects
Velazco, Julio Gabriel
Sorgos
Mejora Genética
Fitomejoramiento
Forrajes
Sorghum Grain
Genetic Gain
Plant Breeding
Forage
title_short Genomic prediction for broad and specific adaptation in sorghum accommodating differential variances of SNP effects
title_full Genomic prediction for broad and specific adaptation in sorghum accommodating differential variances of SNP effects
title_fullStr Genomic prediction for broad and specific adaptation in sorghum accommodating differential variances of SNP effects
title_full_unstemmed Genomic prediction for broad and specific adaptation in sorghum accommodating differential variances of SNP effects
title_sort Genomic prediction for broad and specific adaptation in sorghum accommodating differential variances of SNP effects
dc.creator.none.fl_str_mv Velazco, Julio Gabriel
Jordan, David R.
Hunt, Colleen H.
Mace, Emma S.
van Eeuwijk, Fred A.
author Velazco, Julio Gabriel
author_facet Velazco, Julio Gabriel
Jordan, David R.
Hunt, Colleen H.
Mace, Emma S.
van Eeuwijk, Fred A.
author_role author
author2 Jordan, David R.
Hunt, Colleen H.
Mace, Emma S.
van Eeuwijk, Fred A.
author2_role author
author
author
author
dc.subject.none.fl_str_mv Sorgos
Mejora Genética
Fitomejoramiento
Forrajes
Sorghum Grain
Genetic Gain
Plant Breeding
Forage
topic Sorgos
Mejora Genética
Fitomejoramiento
Forrajes
Sorghum Grain
Genetic Gain
Plant Breeding
Forage
dc.description.none.fl_txt_mv This paper reports a first study exploring genomic prediction for adaptation of sorghum [Sorghum bicolor (L.) Moench] to drought‐stress (D‐ET) and non‐stress (W‐ET) environment types. The objective was to evaluate the impact of both modeling genotype‐by‐environment interaction (G × E) and accounting for heterogeneous variances of marker effects on genomic prediction of parental breeding values for grain yield within and across environment types (ET). For this aim, different genetic covariance structures and different weights for individual markers were investigated in BLUP‐based prediction models. The BLUP models used a kinship matrix combining pedigree and genomic information, termed K‐BLUP. The dataset comprised testcross yield performances under D‐ET and W‐ET as well as pedigree and genomic data. In general, modeling G × E increased predictive ability and reduced empirical bias of genomic predictions for broad adaptation across both ETs compared to models that ignored G × E by fitting a main genetic effect only. Genomic predictions for specific adaptation to D‐ET or to W‐ET were also improved by K‐BLUP models that explicitly accommodated G × E and used data from both ETs, relative to prediction models that used data from the targeted ET exclusively or models that used all the data but assumed no G × E. Allowing for heterogeneous marker variances through weighted K‐BLUP produced clear increments (between 43% and 72%) in predictive ability of genomic prediction for grain yield in all adaptation scenarios. We conclude that G × E as well as locus‐specific genetic variances should be accommodated in genomic prediction models to improve adaptability of sorghum to variable environmental conditions.
EEA Pergamino
Fil: Velazco, Julio. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino. Sección Forrajeras; Argentina. Wageningen University and Research . Biometris – Mathematical and Statistical Methods; Holanda
Fil: Jordan, David R. The University of Queensland. Hermitage Research Facility. Queensland Alliance for Agriculture and Food Innovation; Australia
Fil: Hunt, Colleen H. The University of Queensland. Hermitage Research Facility. Queensland Alliance for Agriculture and Food Innovation; Australia. Hermitage Research Facility. Department of Agriculture and Fisheries; Australia
Fil: Mace, Emma S. The University of Queensland. Hermitage Research Facility. Queensland Alliance for Agriculture and Food Innovation; Australia. Hermitage Research Facility. Department of Agriculture and Fisheries; Australia
Fil: Eeuwijk, Fred A. van. Wageningen University and Research . Biometris – Mathematical and Statistical Methods; Holanda
description This paper reports a first study exploring genomic prediction for adaptation of sorghum [Sorghum bicolor (L.) Moench] to drought‐stress (D‐ET) and non‐stress (W‐ET) environment types. The objective was to evaluate the impact of both modeling genotype‐by‐environment interaction (G × E) and accounting for heterogeneous variances of marker effects on genomic prediction of parental breeding values for grain yield within and across environment types (ET). For this aim, different genetic covariance structures and different weights for individual markers were investigated in BLUP‐based prediction models. The BLUP models used a kinship matrix combining pedigree and genomic information, termed K‐BLUP. The dataset comprised testcross yield performances under D‐ET and W‐ET as well as pedigree and genomic data. In general, modeling G × E increased predictive ability and reduced empirical bias of genomic predictions for broad adaptation across both ETs compared to models that ignored G × E by fitting a main genetic effect only. Genomic predictions for specific adaptation to D‐ET or to W‐ET were also improved by K‐BLUP models that explicitly accommodated G × E and used data from both ETs, relative to prediction models that used data from the targeted ET exclusively or models that used all the data but assumed no G × E. Allowing for heterogeneous marker variances through weighted K‐BLUP produced clear increments (between 43% and 72%) in predictive ability of genomic prediction for grain yield in all adaptation scenarios. We conclude that G × E as well as locus‐specific genetic variances should be accommodated in genomic prediction models to improve adaptability of sorghum to variable environmental conditions.
publishDate 2020
dc.date.none.fl_str_mv 2020-07-23T13:29:25Z
2020-07-23T13:29:25Z
2020-05
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/acceptedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str acceptedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/7601
https://acsess.onlinelibrary.wiley.com/doi/abs/10.1002/csc2.20221
1435-0653 (online)
https://doi.org/10.1002/csc2.20221
url http://hdl.handle.net/20.500.12123/7601
https://acsess.onlinelibrary.wiley.com/doi/abs/10.1002/csc2.20221
https://doi.org/10.1002/csc2.20221
identifier_str_mv 1435-0653 (online)
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
eu_rights_str_mv restrictedAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv American Society of Agronomy
publisher.none.fl_str_mv American Society of Agronomy
dc.source.none.fl_str_mv Crop Science 60 (3) : 1-33 (May -June 2020)
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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