Plant & Animal Genomes XVII Conference

January 10-14, 2009
Town & Country Convention Center
San Diego, CA

454 Sequencing Of Selected Gene Segments In Diverse Barley Germplasm: Is Sequencing Better Than SNP Genotyping?

Andy Flavell¹ , Naeem Syed¹ , Linda Cardle² , Micha Bayer² , David Marshall² , Robbie Waugh²

¹  Division of Plant Sciences, University of Dundee at SCRI, Invergowrie, Dundee DD2 5DA, Scotland, UK

²  Genetics Programme, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK

205 mapped, dispersed barley gene loci fragments, all of which are represented in the barley OPA1 Illumina SNP array have been amplified from 96 diverse barley samples, including cultivars, landraces and wild barleys, using a new method that avoids using roughly more than 20,000 tagged PCR primers and PCRs (see Poster by us in Allele Mining and Genomic Diversity). We will present the sequence data obtained from 454 sequencing of these amplicons and discuss; i) The technical issues of sequencing amplicon pools (e.g. skewed representation of sequences and/or samples); ii) The effectiveness of the extra depth of diversity information obtained over that already available for the Illumina OPA genotyping approach – is it worth the extra trouble and what extra information do we get?