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Extensive natural variation exists for carotenoids in maize grain. Here, to understand its genetic basis, we conducted a joint linkage and genome-wide association study of the US maize nested association mapping panel. Eleven of the 44 detected quantitative trait loci (QTL) were resolved to individual genes. Six of these were correlated expression and effect QTL (ceeQTL), showing strong correlations between RNA-seq expression abundances and QTL allelic effect estimates across six stages of grain development. These six ceeQTL also had the largest percentage of phenotypic variance explained, and in major part comprised the three to five loci capturing the bulk of genetic variation for each trait. Most of these ceeQTL had strongly correlated QTL allelic effect estimates across multiple traits. These findings provide an in-depth genome-level understanding of the genetic and molecular control of carotenoids in plants. In addition, these findings provide a roadmap to accelerate breeding for provitamin A and other priority carotenoid traits in maize grain that should be readily extendable to other cereals.<\/jats:p>","DOI":"10.1093\/plcell\/koab032","type":"journal-article","created":{"date-parts":[[2021,1,28]],"date-time":"2021-01-28T12:55:10Z","timestamp":1611838510000},"page":"882-900","source":"Crossref","is-referenced-by-count":55,"title":["Eleven biosynthetic genes explain the majority of natural variation in carotenoid levels in maize grain"],"prefix":"10.1093","volume":"33","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8411-0343","authenticated-orcid":false,"given":"Christine H","family":"Diepenbrock","sequence":"first","affiliation":[{"name":"Department of Plant Sciences, University of California, Davis, California 95616"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7497-9109","authenticated-orcid":false,"given":"Daniel C","family":"Ilut","sequence":"additional","affiliation":[{"name":"Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5826-6897","authenticated-orcid":false,"given":"Maria","family":"Magallanes-Lundback","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2204-033X","authenticated-orcid":false,"given":"Catherine B","family":"Kandianis","sequence":"additional","affiliation":[{"name":"Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853"},{"name":"Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander E","family":"Lipka","sequence":"additional","affiliation":[{"name":"Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3825-8480","authenticated-orcid":false,"given":"Peter J","family":"Bradbury","sequence":"additional","affiliation":[{"name":"Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853"},{"name":"United States Department of Agriculture\u2014Agricultural Research Service, Robert W. 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