Large Effect QTL for the Timing of Vegetative Phase Change Detected in a Maize Nested Association Mapping Population and Wisconsin Diversity Panel

Vegetative phase change is an intrinsic component of developmental programing in plants. Juvenile and adult vegetative tissues in grasses differ dramatically in their anatomical and biochemical composition, which affects the potential utility of specific genotypes for use as animal feed and biofuel feedstocks. In this study, we assessed the presence of epicuticular wax as an entry point to discover quantitative trait loci (QTL) controlling phenotypic variation for the developmental timing of juvenile to adult transition in two maize mapping populations.  We scored the last leaf with epicuticular wax on the 25 recombinant inbred line families of the Nested Association Mapping (NAM) population and inbred lines from the Wisconsin Diversity Panel across multiple seasons. A total of 13 unique QTL were identified through genome wide analysis across the NAM populations, two of which have large effects, explaining 38.6% of the phenotypic variation. A QTL located on chromosome 9 had the most significant SNPs within Glossy15, a gene controlling expression of adult leaf traits. The second novel large effect QTL was located on chromosome 2.  Association analysis in the diversity panel detected the chromosome 9 QTL only, likely due to the fact that the early-transitioning allele is rare and specific to B73 and related lines.  Our results demonstrate how allele frequency and effect can influence the ability to detect QTL in structured and diverse mapping populations. Furthermore, analysis of natural variation has allowed detection of a novel candidate gene controlling vegetative transition.