A First Generation Haplotype Map of Maize

Twenty-seven diverse maize inbred lines were sequenced using Illumina GA technology in order to define regions of the genome with reduced genetic diversity, reduced historical recombination or increased genetic differentiation between tropical and temparate regions. The relationship of these regions to pericentromeric regions, selective sweeps during maize domestication and improvement, and divergent selection during the geographic expansion of maize are discussed. Suppressed genetic diversity and historical recombination in large pericentromeric regions on each chromosome may play an important role in heterosis. Implications of these results for the prospect of Genome-Wide association analysis in maize and other crops is discussed.