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A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels
Efforts are underway for development of crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency. As a global staple crop with considerable variation in kernel carotenoid composition, maize (Zea mays L.) could have a widespread impact. We performed a genome-...
Autores principales: | , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256781/ https://www.ncbi.nlm.nih.gov/pubmed/25258377 http://dx.doi.org/10.1534/genetics.114.169979 |
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author | Owens, Brenda F. Lipka, Alexander E. Magallanes-Lundback, Maria Tiede, Tyler Diepenbrock, Christine H. Kandianis, Catherine B. Kim, Eunha Cepela, Jason Mateos-Hernandez, Maria Buell, C. Robin Buckler, Edward S. DellaPenna, Dean Gore, Michael A. Rocheford, Torbert |
author_facet | Owens, Brenda F. Lipka, Alexander E. Magallanes-Lundback, Maria Tiede, Tyler Diepenbrock, Christine H. Kandianis, Catherine B. Kim, Eunha Cepela, Jason Mateos-Hernandez, Maria Buell, C. Robin Buckler, Edward S. DellaPenna, Dean Gore, Michael A. Rocheford, Torbert |
author_sort | Owens, Brenda F. |
collection | PubMed |
description | Efforts are underway for development of crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency. As a global staple crop with considerable variation in kernel carotenoid composition, maize (Zea mays L.) could have a widespread impact. We performed a genome-wide association study (GWAS) of quantified seed carotenoids across a panel of maize inbreds ranging from light yellow to dark orange in grain color to identify some of the key genes controlling maize grain carotenoid composition. Significant associations at the genome-wide level were detected within the coding regions of zep1 and lut1, carotenoid biosynthetic genes not previously shown to impact grain carotenoid composition in association studies, as well as within previously associated lcyE and crtRB1 genes. We leveraged existing biochemical and genomic information to identify 58 a priori candidate genes relevant to the biosynthesis and retention of carotenoids in maize to test in a pathway-level analysis. This revealed dxs2 and lut5, genes not previously associated with kernel carotenoids. In genomic prediction models, use of markers that targeted a small set of quantitative trait loci associated with carotenoid levels in prior linkage studies were as effective as genome-wide markers for predicting carotenoid traits. Based on GWAS, pathway-level analysis, and genomic prediction studies, we outline a flexible strategy involving use of a small number of genes that can be selected for rapid conversion of elite white grain germplasm, with minimal amounts of carotenoids, to orange grain versions containing high levels of provitamin A. |
format | Online Article Text |
id | pubmed-4256781 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-42567812014-12-08 A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels Owens, Brenda F. Lipka, Alexander E. Magallanes-Lundback, Maria Tiede, Tyler Diepenbrock, Christine H. Kandianis, Catherine B. Kim, Eunha Cepela, Jason Mateos-Hernandez, Maria Buell, C. Robin Buckler, Edward S. DellaPenna, Dean Gore, Michael A. Rocheford, Torbert Genetics Investigations Efforts are underway for development of crops with improved levels of provitamin A carotenoids to help combat dietary vitamin A deficiency. As a global staple crop with considerable variation in kernel carotenoid composition, maize (Zea mays L.) could have a widespread impact. We performed a genome-wide association study (GWAS) of quantified seed carotenoids across a panel of maize inbreds ranging from light yellow to dark orange in grain color to identify some of the key genes controlling maize grain carotenoid composition. Significant associations at the genome-wide level were detected within the coding regions of zep1 and lut1, carotenoid biosynthetic genes not previously shown to impact grain carotenoid composition in association studies, as well as within previously associated lcyE and crtRB1 genes. We leveraged existing biochemical and genomic information to identify 58 a priori candidate genes relevant to the biosynthesis and retention of carotenoids in maize to test in a pathway-level analysis. This revealed dxs2 and lut5, genes not previously associated with kernel carotenoids. In genomic prediction models, use of markers that targeted a small set of quantitative trait loci associated with carotenoid levels in prior linkage studies were as effective as genome-wide markers for predicting carotenoid traits. Based on GWAS, pathway-level analysis, and genomic prediction studies, we outline a flexible strategy involving use of a small number of genes that can be selected for rapid conversion of elite white grain germplasm, with minimal amounts of carotenoids, to orange grain versions containing high levels of provitamin A. Genetics Society of America 2014-12 2014-09-25 /pmc/articles/PMC4256781/ /pubmed/25258377 http://dx.doi.org/10.1534/genetics.114.169979 Text en Copyright © 2014 by the Genetics Society of America Available freely online through the author-supported open access option. |
spellingShingle | Investigations Owens, Brenda F. Lipka, Alexander E. Magallanes-Lundback, Maria Tiede, Tyler Diepenbrock, Christine H. Kandianis, Catherine B. Kim, Eunha Cepela, Jason Mateos-Hernandez, Maria Buell, C. Robin Buckler, Edward S. DellaPenna, Dean Gore, Michael A. Rocheford, Torbert A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels |
title | A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels |
title_full | A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels |
title_fullStr | A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels |
title_full_unstemmed | A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels |
title_short | A Foundation for Provitamin A Biofortification of Maize: Genome-Wide Association and Genomic Prediction Models of Carotenoid Levels |
title_sort | foundation for provitamin a biofortification of maize: genome-wide association and genomic prediction models of carotenoid levels |
topic | Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256781/ https://www.ncbi.nlm.nih.gov/pubmed/25258377 http://dx.doi.org/10.1534/genetics.114.169979 |
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