Multi-trait genomic prediction model increased the predictive ability for agronomic and malting quality traits in barley (Hordeum vulgare L.)

BHATTA, MADHAV - GUTIÉRREZ, LUCÍA - CAMMAROTA RICCO, LORENA - CARDOZO, FERNANDA - GERMAN, SILVIA - GÓMEZ GUERRERO, BLANCA - PARDO, MARÍA FERNANDA - LANARO, VALERIA - SAYAS, MERCEDES - CASTRO, ARIEL J.

Resumen:

Plant breeders regularly evaluate multiple traits across multiple environments, which opens an avenue for using multiple traits in genomic prediction models. We assessed the potential of multi-trait (MT) genomic prediction model through evaluating several strategies of incorporating multiple traits (eight agronomic and malting quality traits) into the prediction models with two cross-validation schemes (CV1, predicting new lines with genotypic information only and CV2, predicting partially phenotyped lines using both genotypic and phenotypic information from correlated traits) in barley. The predictive ability was similar for single (ST-CV1) and multi-trait (MT-CV1) models to predict new lines. However, the predictive ability for agronomic traits was considerably increased when partially phenotyped lines (MT-CV2) were used. The predictive ability for grain yield using the MT-CV2 model with other agronomic traits resulted in 57% and 61% higher predictive ability than ST-CV1 and MT-CV1 models, respectively. Therefore, complex traits such as grain yield are better predicted when correlated traits are used. Similarly, a considerable increase in the predictive ability of malting quality traits was observed when correlated traits were used. The predictive ability for grain protein content using the MT-CV2 model with both agronomic and malting traits resulted in a 76% higher predictive ability than ST-CV1 and MT-CV1 models. Additionally, the higher predictive ability for new environments was obtained for all traits using the MT-CV2 model compared to the MT-CV1 model. This study showed the potential of improving the genomic prediction of complex traits by incorporating the information from multiple traits (cost-friendly and easy to measure traits) collected throughout breeding programs which could assist in speeding up breeding cycles


Detalles Bibliográficos
2020
CEBADA
GENOTIPO
Inglés
Laboratorio Tecnológico del Uruguay
Catálogo digital del LATU
https://catalogo.latu.org.uy/opac_css/index.php?lvl=notice_display&id=32416
Acceso abierto
CC BY
_version_ 1807353831786283008
author BHATTA, MADHAV
author2 GUTIÉRREZ, LUCÍA
CAMMAROTA RICCO, LORENA
CARDOZO, FERNANDA
GERMAN, SILVIA
GÓMEZ GUERRERO, BLANCA
PARDO, MARÍA FERNANDA
LANARO, VALERIA
SAYAS, MERCEDES
CASTRO, ARIEL J.
author2_role author
author
author
author
author
author
author
author
author
author_facet BHATTA, MADHAV
GUTIÉRREZ, LUCÍA
CAMMAROTA RICCO, LORENA
CARDOZO, FERNANDA
GERMAN, SILVIA
GÓMEZ GUERRERO, BLANCA
PARDO, MARÍA FERNANDA
LANARO, VALERIA
SAYAS, MERCEDES
CASTRO, ARIEL J.
author_role author
collection Catálogo digital del LATU
dc.coverage.none.fl_str_mv En: G3: Genes, Genomes, Genetics, 10(3), pp.1113-1124. DOI: 10.1177/1082013219853489
dc.creator.none.fl_str_mv BHATTA, MADHAV
GUTIÉRREZ, LUCÍA
CAMMAROTA RICCO, LORENA
CARDOZO, FERNANDA
GERMAN, SILVIA
GÓMEZ GUERRERO, BLANCA
PARDO, MARÍA FERNANDA
LANARO, VALERIA
SAYAS, MERCEDES
CASTRO, ARIEL J.
dc.date.none.fl_str_mv 2020-01-01
dc.description.abstract.none.fl_txt_mv Plant breeders regularly evaluate multiple traits across multiple environments, which opens an avenue for using multiple traits in genomic prediction models. We assessed the potential of multi-trait (MT) genomic prediction model through evaluating several strategies of incorporating multiple traits (eight agronomic and malting quality traits) into the prediction models with two cross-validation schemes (CV1, predicting new lines with genotypic information only and CV2, predicting partially phenotyped lines using both genotypic and phenotypic information from correlated traits) in barley. The predictive ability was similar for single (ST-CV1) and multi-trait (MT-CV1) models to predict new lines. However, the predictive ability for agronomic traits was considerably increased when partially phenotyped lines (MT-CV2) were used. The predictive ability for grain yield using the MT-CV2 model with other agronomic traits resulted in 57% and 61% higher predictive ability than ST-CV1 and MT-CV1 models, respectively. Therefore, complex traits such as grain yield are better predicted when correlated traits are used. Similarly, a considerable increase in the predictive ability of malting quality traits was observed when correlated traits were used. The predictive ability for grain protein content using the MT-CV2 model with both agronomic and malting traits resulted in a 76% higher predictive ability than ST-CV1 and MT-CV1 models. Additionally, the higher predictive ability for new environments was obtained for all traits using the MT-CV2 model compared to the MT-CV1 model. This study showed the potential of improving the genomic prediction of complex traits by incorporating the information from multiple traits (cost-friendly and easy to measure traits) collected throughout breeding programs which could assist in speeding up breeding cycles
dc.format.none.fl_str_mv Pdf
dc.identifier.none.fl_str_mv https://catalogo.latu.org.uy/opac_css/index.php?lvl=notice_display&id=32416
32416
urn:ISBN:69387
dc.language.iso.none.fl_str_mv eng
dc.rights.license.none.fl_str_mv CC BY
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
CC BY
dc.source.none.fl_str_mv reponame:Catálogo digital del LATU
instname:Laboratorio Tecnológico del Uruguay
instacron:Laboratorio Tecnológico del Uruguay
dc.subject.none.fl_str_mv CEBADA
GENOTIPO
dc.title.none.fl_str_mv Multi-trait genomic prediction model increased the predictive ability for agronomic and malting quality traits in barley (Hordeum vulgare L.)
dc.type.none.fl_str_mv info:eu-repo/semantics/article
Publicado
dc.type.version.none.fl_str_mv info:eu-repo/semantics/publishedVersion
description Plant breeders regularly evaluate multiple traits across multiple environments, which opens an avenue for using multiple traits in genomic prediction models. We assessed the potential of multi-trait (MT) genomic prediction model through evaluating several strategies of incorporating multiple traits (eight agronomic and malting quality traits) into the prediction models with two cross-validation schemes (CV1, predicting new lines with genotypic information only and CV2, predicting partially phenotyped lines using both genotypic and phenotypic information from correlated traits) in barley. The predictive ability was similar for single (ST-CV1) and multi-trait (MT-CV1) models to predict new lines. However, the predictive ability for agronomic traits was considerably increased when partially phenotyped lines (MT-CV2) were used. The predictive ability for grain yield using the MT-CV2 model with other agronomic traits resulted in 57% and 61% higher predictive ability than ST-CV1 and MT-CV1 models, respectively. Therefore, complex traits such as grain yield are better predicted when correlated traits are used. Similarly, a considerable increase in the predictive ability of malting quality traits was observed when correlated traits were used. The predictive ability for grain protein content using the MT-CV2 model with both agronomic and malting traits resulted in a 76% higher predictive ability than ST-CV1 and MT-CV1 models. Additionally, the higher predictive ability for new environments was obtained for all traits using the MT-CV2 model compared to the MT-CV1 model. This study showed the potential of improving the genomic prediction of complex traits by incorporating the information from multiple traits (cost-friendly and easy to measure traits) collected throughout breeding programs which could assist in speeding up breeding cycles
eu_rights_str_mv openAccess
format article
id LATU_5adfe47f12a99475530b4d136446a2e4
identifier_str_mv 32416
urn:ISBN:69387
instacron_str Laboratorio Tecnológico del Uruguay
institution Laboratorio Tecnológico del Uruguay
instname_str Laboratorio Tecnológico del Uruguay
language eng
network_acronym_str LATU
network_name_str Catálogo digital del LATU
oai_identifier_str oai:PMBOAI:32416
publishDate 2020
reponame_str Catálogo digital del LATU
repository.mail.fl_str_mv lfiori@latu.org.uy
repository.name.fl_str_mv Catálogo digital del LATU - Laboratorio Tecnológico del Uruguay
repository_id_str
rights_invalid_str_mv CC BY
CC BY
spelling Multi-trait genomic prediction model increased the predictive ability for agronomic and malting quality traits in barley (Hordeum vulgare L.)BHATTA, MADHAVGUTIÉRREZ, LUCÍACAMMAROTA RICCO, LORENACARDOZO, FERNANDAGERMAN, SILVIAGÓMEZ GUERRERO, BLANCAPARDO, MARÍA FERNANDALANARO, VALERIASAYAS, MERCEDESCASTRO, ARIEL J.CEBADAGENOTIPOPlant breeders regularly evaluate multiple traits across multiple environments, which opens an avenue for using multiple traits in genomic prediction models. We assessed the potential of multi-trait (MT) genomic prediction model through evaluating several strategies of incorporating multiple traits (eight agronomic and malting quality traits) into the prediction models with two cross-validation schemes (CV1, predicting new lines with genotypic information only and CV2, predicting partially phenotyped lines using both genotypic and phenotypic information from correlated traits) in barley. The predictive ability was similar for single (ST-CV1) and multi-trait (MT-CV1) models to predict new lines. However, the predictive ability for agronomic traits was considerably increased when partially phenotyped lines (MT-CV2) were used. The predictive ability for grain yield using the MT-CV2 model with other agronomic traits resulted in 57% and 61% higher predictive ability than ST-CV1 and MT-CV1 models, respectively. Therefore, complex traits such as grain yield are better predicted when correlated traits are used. Similarly, a considerable increase in the predictive ability of malting quality traits was observed when correlated traits were used. The predictive ability for grain protein content using the MT-CV2 model with both agronomic and malting traits resulted in a 76% higher predictive ability than ST-CV1 and MT-CV1 models. Additionally, the higher predictive ability for new environments was obtained for all traits using the MT-CV2 model compared to the MT-CV1 model. This study showed the potential of improving the genomic prediction of complex traits by incorporating the information from multiple traits (cost-friendly and easy to measure traits) collected throughout breeding programs which could assist in speeding up breeding cycles2020-01-01info:eu-repo/semantics/articlePublicadoinfo:eu-repo/semantics/publishedVersionPdfhttps://catalogo.latu.org.uy/opac_css/index.php?lvl=notice_display&id=3241632416urn:ISBN:69387engEn: G3: Genes, Genomes, Genetics, 10(3), pp.1113-1124. DOI: 10.1177/1082013219853489 info:eu-repo/semantics/openAccessCC BYCC BYreponame:Catálogo digital del LATUinstname:Laboratorio Tecnológico del Uruguayinstacron:Laboratorio Tecnológico del Uruguay2021-11-17T18:09:27Zoai:PMBOAI:32416Gobiernohttps://latu.org.uy/https://catalogo.latu.org.uy/ws/PMBOAIlfiori@latu.org.uyUruguayopendoar:2024-08-01T14:48:58.858068Catálogo digital del LATU - Laboratorio Tecnológico del Uruguayfalse
spellingShingle Multi-trait genomic prediction model increased the predictive ability for agronomic and malting quality traits in barley (Hordeum vulgare L.)
BHATTA, MADHAV
CEBADA
GENOTIPO
status_str publishedVersion
title Multi-trait genomic prediction model increased the predictive ability for agronomic and malting quality traits in barley (Hordeum vulgare L.)
title_full Multi-trait genomic prediction model increased the predictive ability for agronomic and malting quality traits in barley (Hordeum vulgare L.)
title_fullStr Multi-trait genomic prediction model increased the predictive ability for agronomic and malting quality traits in barley (Hordeum vulgare L.)
title_full_unstemmed Multi-trait genomic prediction model increased the predictive ability for agronomic and malting quality traits in barley (Hordeum vulgare L.)
title_short Multi-trait genomic prediction model increased the predictive ability for agronomic and malting quality traits in barley (Hordeum vulgare L.)
title_sort Multi-trait genomic prediction model increased the predictive ability for agronomic and malting quality traits in barley (Hordeum vulgare L.)
topic CEBADA
GENOTIPO
url https://catalogo.latu.org.uy/opac_css/index.php?lvl=notice_display&id=32416