Approaches to Association Analysis In a Hybrid Context In Maize.

Nearly 2000 inbred maize lines are publicly available in the USDA Germplasm collection, and the density of genotypic information on these lines is increasing.  This resource will have great utility for association genetic analysis.  While the inbreds are genotyped, it is desirable for many traits to evaluate the materials in a hybrid context.  One approach is to topcross all of the lines to one or a few testers, but this can restrict interpretation of genetic effects, and can confound relatedness with performance.  In this research, we are evaluating hybrids produced from randomly paired inbreds as an approach to evaluate genetic effects in a hybrid context.  A set of 627 inbred lines and a population of 672 randomly-mated hybrids produced from the initial set of 627 inbreds, were grown in a completely randomized design with two replicates in 2008 and 2009, respectively.  Population structure was evaluated by both principal component analysis and Structure 2.3.1  based on 511 SNP markers to test the hypothesis that testcross hybrids exhibit identical levels of population structure as inbreds,  where as randomly-mated hybrids exhibit lower levels of structure in relation to inbreds. Phenotypic data was collected for internode length and number, total leaf number, number of leaves to the upper most ear, plant height, ear height, percentage of leaves with epicuticular wax, and flowering time. Results from the analyses of population structure, phenotypic data, and association studies will be reported.