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In collaboration with Doreen Ware (CSHL), Jer-Ming Chia (CSHL) and George Grills (Cornell), we (Mike Gore, Rob Elshire, Elhan Ersoz, and Jason Peiffer) have developed a first generation maize HapMap for the 27 founder lines of NAM (Gore et al. 2009 Science). We used three reduced representation strategies to enrich for low-copy genomic regions and then re-sequenced the resulting libraries using Illumina GA technology (36 base reads). Filtering of the several million polymorphisms for quality resulted in a high quality data set consisting of 1.4 million SNPs and 200,000 indels. Analyses of these data uncovered hundreds of selective sweeps resulting from domestication and/or adaptation and numerous highly differentiated regions that are likely key to geographic adaptation. Our analyses also shed light on the molecular basis of heterosis in maize.
In our previous work with the NAM population (McMullen et al. 2009 Science) we showed that pericentromeric regions had highly suppressed recombination rates but elevated residual heterozygosity relative to the rest of the genome. Our HapMap results (Gore et al. 2009 Science) allowed us to rule out local genetic diversity levels and gene density as potential confounding effects, leaving suppressed recombination as the best explanation for the elevated residual heterozygosity. We theorized that this suppression of recombination in centromeric regions has prevented the co-occurrence, within a single inbred line during modern breeding, of favorable combinations of alleles across multiple pericentromeric genes. Hence, it is only in hybrids that these favorable combinations can be brought together, leading to heterosis.
Our first generation HapMap data are available for download from the Panzea website here. Be forewarned that the data files are large.
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