AbstractPurple corn offers an attractive source of economical natural anthocyanin-based colorant for use in foods and beverages. Yet to maximize the scalability and meet growing demands, both anthocyanin concentrations and agronomic performance must improve in purple corn varieties. We studied flux through the flavonoid biosynthesis pathway using GWAS data derived from a diverse purple corn landrace with anthocyanin-rich pericarp, Apache Red. Trends between flavonoid endpoints suggest that

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... ators of total flux into the pathway and regulators of partitioning within the pathway may both represent targets for maximizing anthocyanin content. A peak at the end of chromosome 1 near Aat1 (Anthocyanin acyltransferase1) was highly significant in all approaches taken to map anthocyanin flux, suggesting the structural modification of malonylation is required for maximal anthocyanin production. We also identified several candidate MATEs and H+ ATPases that could assist in the preferential transport of acylated anthocyanins into the vacuole. These and other candidates identified here suggest there is still much to learn about the regulation of anthocyanin biosynthesis in the pericarp of purple corn. The efficacy of genomic predictions in the population was also studied, yielding an accuracy of 0.71 with cross validation for total anthocyanin content with no improvement found when known anthocyanin regulators were added to the model. These data suggest that genomic selection could be employed effectively in a purple corn breeding program, and especially for a landrace improvement program.