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What are the molecular differences between maize lines? Maize is an incredibly diverse species. Any two maize lines can be as genetically diverse as chimps and humans. Identifying the differences between maize lines at the molecular level is one important part of understanding the variety we see in maize. Nearly 5000 amplicons have been scored in maize and teosinte panels by Sanger sequencing. These are available through the Panzea website. We have transitioned our efforts to next generation sequencing technology with Illumina Genome Analyzers. With our collaborators at Cold Spring Harbor Laboratory (Doreen Ware, Jer-Ming Chia and Bonnie Hurwitz), we have produced over 1 billion lines of maize (NAM founders) and teosinte sequence which is being used to call SNPs. The maize genome consists of 80% repeats and 20% gene space. In order to focus on SNPs in the gene space we constructed reduced representation libraries using HpaII: a methylation sensitive restriction enzyme. See our protocol for the details.
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