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Genome-Wide Association Study and Pathway-Level Analysis of Kernel Color in Maize

Brenda F. Owens, Deepu Mathew, Christine Diepenbrock, Tyler Tiede, Di Wu, Maria Mateos-Hernandez, View ORCID ProfileMichael A. Gore, Torbert Rocheford
doi: https://doi.org/10.1101/535872
Brenda F. Owens
BASF;
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Deepu Mathew
Kerala Agricultural University;
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Christine Diepenbrock
Corteva AgriscienceTM, the Agriculture Division of DowDuPontTM;
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  • For correspondence: chd45@cornell.edu
Tyler Tiede
PepsiCo;
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Di Wu
Cornell University;
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Maria Mateos-Hernandez
Monsanto Company;
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Michael A. Gore
Cornell University;
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Torbert Rocheford
Purdue University
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Abstract

Rapid development and adoption of biofortified, provitamin A-dense orange maize (Zea mays L.) varieties could be facilitated by a greater understanding of the natural variation underlying kernel color, including as relates to carotenoid biosynthesis and retention in maize grain. Greater abundance of carotenoids in maize kernels is generally accompanied by deeper orange color, useful for distinguishing provitamin A-dense varieties to consumers. While kernel color can be scored and selected with high-throughput, low-cost phenotypic methods within breeding selection programs, it remains to be well established as to what would be the logical genetic loci to target for selection for kernel color. We conducted a genome-wide association study of maize kernel color, as determined by colorimetry, in 1,651 yellow and orange inbreds from the Ames maize inbred panel. Associations were found with y1, encoding the first committed step in carotenoid biosynthesis, and with dxs2, which encodes the enzyme responsible for the first committed step in the biosynthesis of the isoprenoid precursors of carotenoids. These genes logically could contribute to overall carotenoid abundance and thus kernel color. The lcyE and zep1 genes, which can affect carotenoid composition, were also found to be associated with colorimeter values. A pathway-level analysis, focused on genes with a priori evidence of involvement in carotenoid biosynthesis and retention, revealed associations for dxs3 and dmes1, involved in isoprenoid biosynthesis; ps1 and vp5, within the core carotenoid pathway; and vp14, involved in cleavage of carotenoids. Collectively, these identified genes appear relevant to the accumulation of kernel color.

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Posted January 30, 2019.
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Genome-Wide Association Study and Pathway-Level Analysis of Kernel Color in Maize
Brenda F. Owens, Deepu Mathew, Christine Diepenbrock, Tyler Tiede, Di Wu, Maria Mateos-Hernandez, Michael A. Gore, Torbert Rocheford
bioRxiv 535872; doi: https://doi.org/10.1101/535872
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Genome-Wide Association Study and Pathway-Level Analysis of Kernel Color in Maize
Brenda F. Owens, Deepu Mathew, Christine Diepenbrock, Tyler Tiede, Di Wu, Maria Mateos-Hernandez, Michael A. Gore, Torbert Rocheford
bioRxiv 535872; doi: https://doi.org/10.1101/535872

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