title: A foundation for provitamin A biofortification of maize: genome-wide association and genomic prediction models of carotenoid levels.
abstract: 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.
authors.affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907.
authors.forename: Brenda F
authors.initials: BF
authors.lastname: Owens
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853 Department of Crop Sciences, University of Illinois, Urbana, Illinois 61801.
authors.forename: Alexander E
authors.initials: AE
authors.lastname: Lipka
authors.affiliation: Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Maria
authors.initials: M
authors.lastname: Magallanes-Lundback
authors.affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907.
authors.forename: Tyler
authors.initials: T
authors.lastname: Tiede
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853.
authors.forename: Christine H
authors.initials: CH
authors.lastname: Diepenbrock
authors.affiliation: Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853.
authors.forename: Catherine B
authors.initials: CB
authors.lastname: Kandianis
authors.affiliation: Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Eunha
authors.initials: E
authors.lastname: Kim
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Jason
authors.initials: J
authors.lastname: Cepela
authors.affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907.
authors.forename: Maria
authors.initials: M
authors.lastname: Mateos-Hernandez
authors.affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
authors.affiliation: Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853 Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 U. S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853.
authors.forename: Edward S
authors.initials: ES
authors.lastname: Buckler
authors.affiliation: Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.
authors.forename: Dean
authors.initials: D
authors.lastname: DellaPenna
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853 torbert@purdue.edu mag87@cornell.edu.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Gore
authors.affiliation: Department of Agronomy, Purdue University, West Lafayette, Indiana 47907 torbert@purdue.edu mag87@cornell.edu.
authors.forename: Torbert
authors.initials: T
authors.lastname: Rocheford
mesh_terms: D053898:Biosynthetic Pathways; D002338:Carotenoids / Q000378:metabolism*; D055106:Genome-Wide Association Study; D023281:Genomics; D015810:Linkage Disequilibrium; D008954:Models, Biological; D010641:Phenotype; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D015203:Reproducibility of Results; D003313:Zea mays / Q000235:genetics* / Q000378:metabolism*
chemical_list: D002338:Carotenoids
keywords: biofortification; carotenoid; genome-wide association study; genomic prediction; pathway-level analysis; provitamin A