Genotyping-By-Sequencing Approaches for Your Favorite Large Polyploidy Genome (Avena sativa)

We have focused on using new sequencing technologies for genotyping in complex polyploidy genomes such as wheat and oat.  Rapid advances in sequencing output make this a promising approach even in these large genomes.  We are using genotyping-by-sequencing (GBS) to produce a reduced genome representation and target polymorphisms in the genomic space flanking restriction enzyme sites.  Combined with multiplexing samples using DNA barcoded adapters, this approach has enabled high-throughput genotyping with relatively low per sample costs.  We have developed GBS protocols and informatics suitable for wheat and have genotyped a range of mapping and breeding populations.  We have then transferred this approach to oat focusing on genotyping two bi-parental populations, Ogle x TAM RILs and Kanota x Ogle  RILs.  We are using a bin mapping approach in these bi-parental populations to map GBS tags and SNPs and develop a reference GBS map for Oat.  GBS is a robust genotyping approach for polyploidy genomes as it facilitates the differentiation and mapping of SNPs in duplicated sequences by taking advantage of genome-specific context sequence.  Though the oat genome presents a formable challenge, the integration of new genomics tools such as GBS are making characterization of these complex genomes more tractable.  Examples of integration of GBS in the development of the barley reference genome will be shown.  Rapid advances in sequencing output will continue to increase the utility of GBS for functional genomics.  Increased sequencing output will also allow higher levels of multiplexing, driving per sample costs lower, further increasing the utility of this approach for genomics assisted breeding.