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
- Institución
- Instituto Nacional de Tecnología Agropecuaria
- OAI Identificador
- oai:localhost:20.500.12123/7601
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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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12.559606 |