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

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 it 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.

Chromosome-level genome assembly of a regenerable maize inbred line A188

“…An additional minor kernel color QTL was identified from the DH lines and concordant with the QTLs from multiple other B73-derived bi-parental populations [ 49 ]. The underlying candidate gene, zep1 (Zm00001d003513) encoding zeaxanthin epoxidase, was also identified in an earlier association study [ 50 ]. However, functional validation for the involvement of zep1 in seed color is needed.…”

Chromosome-level Genome Assembly of a Regenerable Maize Inbred Line A188

“…We have identified an additional minor QTL that was concordant with QTLs from multiple other B73-derived bi-parental populations 42 . The candidate gene zep1 (Zm00001d003513) encoding zeaxanthin epoxidase was previously identified but functional validation is needed 43 . Based on kernel colors of DH lines, the three QTL loci are not sufficient to fully determine kernel colors.…”

Effects of Mass Selection on Husk and Cob Color in Five Purple Field Corn Populations Segregating for Purple Husks

“…Previous studies reported a strong association between kernel color and phytochemicals in corn. Purple color of corn was positively and significantly related to anthocyanins and antioxidant activities [25,49], and visually scored orange kernel color was associated with carotenoids [69,70].…”