Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean.

CRUZ, M. - ARBELAEZ, J. D. - LOAIZA, K. - CUASQUER, J. - ROSAS, J.E. - GRATEROL, E.

Resumen:

AbstractRice (Oryza sativa L.)grain quality is a set of complex interrelated traits that include grain milling, appearance, cooking, and edible properties. As consumer preferences in Latin America and the Caribbean evolve, determining what traits best capture regional grain quality preferences is fundamental for breeding and cultivar release.In this study, a genome-wide association study (GWAS), marker-assisted selection (MAS), and genomic selection (GS) were evaluated to help guide the development of new breeding strategies for rice grain quality improvement. For this purpose, 284 rice lines representing over 20 yr of breeding in Latin America and the Caribbean were genotyped and phenotyped for 10 different traits including grain milling, appearance, cooking, and edible quality traits. Genetic correlations among the 10 traits ranged from ?0.83 to 0.85. A GWAS identified 19 significant marker/trait combinations associated with eight grain quality traits. Four functional markers, three located in the Waxy and one in the starch synthase IIa genes, were significantly associated with six grain-quality traits. These markers individually explained 51?75% of the phenotypic variance depending on the trait, clearly indicating their potential utility for MAS.Cross-validation studies to evaluate predictive abilities of four different GS models for each of the 10 quality traits were conducted and predictive abilities ranged from 0.3 to 0.72. Overall, the machine learning model random forest had the highest predictive abilities and was especially effective for traits where large effect quantitative trait loci were identified. This study provides the foundation for deploying effective molecular breeding strategies for grain quality in Latin American rice breeding programs.


Detalles Bibliográficos
2021
RICE
FITOMEJORAMIENTO
CALIDAD CULINARIA
CALIDAD DE GRANO
CALIDAD DE LA SEMILLA
Inglés
Instituto Nacional de Investigación Agropecuaria
AINFO
http://www.ainfo.inia.uy/consulta/busca?b=pc&id=62397&biblioteca=vazio&busca=62397&qFacets=62397
Acceso abierto
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author CRUZ, M.
author2 ARBELAEZ, J. D.
LOAIZA, K.
CUASQUER, J.
ROSAS, J.E.
GRATEROL, E.
author2_role author
author
author
author
author
author_facet CRUZ, M.
ARBELAEZ, J. D.
LOAIZA, K.
CUASQUER, J.
ROSAS, J.E.
GRATEROL, E.
author_role author
bitstream.checksum.fl_str_mv c495e93e64a9a444ff5c459177fe0b1a
bitstream.checksumAlgorithm.fl_str_mv MD5
bitstream.url.fl_str_mv https://redi.anii.org.uy/jspui/bitstream/20.500.12381/1930/1/sword-2022-10-20T22%3a55%3a15.original.xml
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dc.creator.none.fl_str_mv CRUZ, M.
ARBELAEZ, J. D.
LOAIZA, K.
CUASQUER, J.
ROSAS, J.E.
GRATEROL, E.
dc.date.accessioned.none.fl_str_mv 2022-10-21T01:55:15Z
dc.date.available.none.fl_str_mv 2022-10-21T01:55:15Z
dc.date.issued.none.fl_str_mv 2021
dc.date.updated.none.fl_str_mv 2022-10-21T01:55:15Z
dc.description.abstract.none.fl_txt_mv AbstractRice (Oryza sativa L.)grain quality is a set of complex interrelated traits that include grain milling, appearance, cooking, and edible properties. As consumer preferences in Latin America and the Caribbean evolve, determining what traits best capture regional grain quality preferences is fundamental for breeding and cultivar release.In this study, a genome-wide association study (GWAS), marker-assisted selection (MAS), and genomic selection (GS) were evaluated to help guide the development of new breeding strategies for rice grain quality improvement. For this purpose, 284 rice lines representing over 20 yr of breeding in Latin America and the Caribbean were genotyped and phenotyped for 10 different traits including grain milling, appearance, cooking, and edible quality traits. Genetic correlations among the 10 traits ranged from ?0.83 to 0.85. A GWAS identified 19 significant marker/trait combinations associated with eight grain quality traits. Four functional markers, three located in the Waxy and one in the starch synthase IIa genes, were significantly associated with six grain-quality traits. These markers individually explained 51?75% of the phenotypic variance depending on the trait, clearly indicating their potential utility for MAS.Cross-validation studies to evaluate predictive abilities of four different GS models for each of the 10 quality traits were conducted and predictive abilities ranged from 0.3 to 0.72. Overall, the machine learning model random forest had the highest predictive abilities and was especially effective for traits where large effect quantitative trait loci were identified. This study provides the foundation for deploying effective molecular breeding strategies for grain quality in Latin American rice breeding programs.
dc.identifier.none.fl_str_mv http://www.ainfo.inia.uy/consulta/busca?b=pc&id=62397&biblioteca=vazio&busca=62397&qFacets=62397
dc.language.iso.none.fl_str_mv en
eng
dc.rights.es.fl_str_mv Acceso abierto
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
dc.source.none.fl_str_mv reponame:AINFO
instname:Instituto Nacional de Investigación Agropecuaria
instacron:Instituto Nacional de Investigación Agropecuaria
dc.subject.none.fl_str_mv RICE
FITOMEJORAMIENTO
CALIDAD CULINARIA
CALIDAD DE GRANO
CALIDAD DE LA SEMILLA
dc.title.none.fl_str_mv Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean.
dc.type.none.fl_str_mv Article
PublishedVersion
info:eu-repo/semantics/article
dc.type.version.none.fl_str_mv info:eu-repo/semantics/publishedVersion
description AbstractRice (Oryza sativa L.)grain quality is a set of complex interrelated traits that include grain milling, appearance, cooking, and edible properties. As consumer preferences in Latin America and the Caribbean evolve, determining what traits best capture regional grain quality preferences is fundamental for breeding and cultivar release.In this study, a genome-wide association study (GWAS), marker-assisted selection (MAS), and genomic selection (GS) were evaluated to help guide the development of new breeding strategies for rice grain quality improvement. For this purpose, 284 rice lines representing over 20 yr of breeding in Latin America and the Caribbean were genotyped and phenotyped for 10 different traits including grain milling, appearance, cooking, and edible quality traits. Genetic correlations among the 10 traits ranged from ?0.83 to 0.85. A GWAS identified 19 significant marker/trait combinations associated with eight grain quality traits. Four functional markers, three located in the Waxy and one in the starch synthase IIa genes, were significantly associated with six grain-quality traits. These markers individually explained 51?75% of the phenotypic variance depending on the trait, clearly indicating their potential utility for MAS.Cross-validation studies to evaluate predictive abilities of four different GS models for each of the 10 quality traits were conducted and predictive abilities ranged from 0.3 to 0.72. Overall, the machine learning model random forest had the highest predictive abilities and was especially effective for traits where large effect quantitative trait loci were identified. This study provides the foundation for deploying effective molecular breeding strategies for grain quality in Latin American rice breeding programs.
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spelling 2022-10-21T01:55:15Z2022-10-21T01:55:15Z20212022-10-21T01:55:15Zhttp://www.ainfo.inia.uy/consulta/busca?b=pc&id=62397&biblioteca=vazio&busca=62397&qFacets=62397AbstractRice (Oryza sativa L.)grain quality is a set of complex interrelated traits that include grain milling, appearance, cooking, and edible properties. As consumer preferences in Latin America and the Caribbean evolve, determining what traits best capture regional grain quality preferences is fundamental for breeding and cultivar release.In this study, a genome-wide association study (GWAS), marker-assisted selection (MAS), and genomic selection (GS) were evaluated to help guide the development of new breeding strategies for rice grain quality improvement. For this purpose, 284 rice lines representing over 20 yr of breeding in Latin America and the Caribbean were genotyped and phenotyped for 10 different traits including grain milling, appearance, cooking, and edible quality traits. Genetic correlations among the 10 traits ranged from ?0.83 to 0.85. A GWAS identified 19 significant marker/trait combinations associated with eight grain quality traits. Four functional markers, three located in the Waxy and one in the starch synthase IIa genes, were significantly associated with six grain-quality traits. These markers individually explained 51?75% of the phenotypic variance depending on the trait, clearly indicating their potential utility for MAS.Cross-validation studies to evaluate predictive abilities of four different GS models for each of the 10 quality traits were conducted and predictive abilities ranged from 0.3 to 0.72. Overall, the machine learning model random forest had the highest predictive abilities and was especially effective for traits where large effect quantitative trait loci were identified. This study provides the foundation for deploying effective molecular breeding strategies for grain quality in Latin American rice breeding programs.https://hdl.handle.net/20.500.12381/1930enenginfo:eu-repo/semantics/openAccessAcceso abiertoRICEFITOMEJORAMIENTOCALIDAD CULINARIACALIDAD DE GRANOCALIDAD DE LA SEMILLAGenetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean.ArticlePublishedVersioninfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionreponame:AINFOinstname:Instituto Nacional de Investigación Agropecuariainstacron:Instituto Nacional de Investigación AgropecuariaCRUZ, M.ARBELAEZ, J. D.LOAIZA, K.CUASQUER, J.ROSAS, J.E.GRATEROL, E.SWORDsword-2022-10-20T22:55:15.original.xmlOriginal SWORD entry documentapplication/octet-stream3106https://redi.anii.org.uy/jspui/bitstream/20.500.12381/1930/1/sword-2022-10-20T22%3a55%3a15.original.xmlc495e93e64a9a444ff5c459177fe0b1aMD5120.500.12381/19302022-10-20 22:55:15.975oai:redi.anii.org.uy:20.500.12381/1930Gobiernohttp://inia.uyhttps://redi.anii.org.uy/oai/requestlorrego@inia.org.uyUruguayopendoar:2022-10-21T01:55:15AINFO - Instituto Nacional de Investigación Agropecuariafalse
spellingShingle Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean.
CRUZ, M.
RICE
FITOMEJORAMIENTO
CALIDAD CULINARIA
CALIDAD DE GRANO
CALIDAD DE LA SEMILLA
status_str publishedVersion
title Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean.
title_full Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean.
title_fullStr Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean.
title_full_unstemmed Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean.
title_short Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean.
title_sort Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean.
topic RICE
FITOMEJORAMIENTO
CALIDAD CULINARIA
CALIDAD DE GRANO
CALIDAD DE LA SEMILLA
url http://www.ainfo.inia.uy/consulta/busca?b=pc&id=62397&biblioteca=vazio&busca=62397&qFacets=62397