Maize_HapMap_1
A First Generation Haplotype Map of Maize
Maize (Zea mays L.) is an important crop species of high genetic diversity. We identified and genotyped several million sequence polymorphisms among 27 diverse maize inbred lines and discovered that the genome was characterized by highly divergent haplotypes, and showed 10 to 30-fold variation in recombination rates. Most chromosomes have pericentromeric regions with highly suppressed recombination, which appear to have impacted the effectiveness of selection during maize inbred development and may be a major component of heterosis. We found more than a hundred selective sweeps, many over 1 Mbp in size, and almost 200 highly differentiated regions that likely contain loci key to geographic adaptation. This survey of genetic diversity provides a foundation for uniting breeding efforts across the world and for dissecting complex traits through Genome-Wide Association Studies (GWAS).
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.