SNP discovery in microsatellites and ESTs in hexaploid wheat using Pyrosequencing.

摘要

As participants in the International Wheat SNP Consortium, we are using the ability of Pyrosequencing to distinguish between varieties with a base variant in only one of three genomes to validate the presence of SNPs which are indicated by the comparative alignment of published wheat ESTs. In addition we are exploring the frequency of SNPs in microsatellite flanking regions. In wheat, hundreds of mapped microsatellites are available. Each successful result will be a SNP with a known map location. Although SNPs can be exploited using well-established technologies, their discovery requires that sequences from several varieties be compared. In species such as hexaploid wheat the polymorphism is likely-only to be present in one of the three genomes. Forthis reason we need to reveal differences between varieties of the proportionate presence of variant bases. Although Pyrosequencing is used for short sequences, the Pyrogram fingerprint will indicate the presence of variant bases in hexaploid wheat. Itis therefore ideally suited to SNP discovery in the small flanking regions available in most wheat microsatellite markers. Once SNPs are discovered they can be applied to specific varieties of wheat and exploited for variety identification or trait association using more commonly available technology.