Genotyping-By-Sequencing to Enable Genomics Assisted Breeding in Wheat

Rapid advances in sequencing technology have opened new possibilities for using genomic information in breeding and genetic studies in complex genomes such as wheat.  Genotyping-by-sequencing (GBS) uses reduced representation sequencing by targeting 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 are using bi-parental populations to map GBS tags and SNPs.  By combining different mapping populations we are developing a reference genetic map of sequence tags that will be useful for association genetics and genomic selection as well as anchoring and ordering genomic sequence. The GBS approach also facilitates the differentiation and mapping of duplicated sequences within large complex genomes.  We have genotyped a large set of breeding lines from the CIMMYT international wheat breeding programs and are developing prediction models for genomic selection.  The GBS approach will then be used to genotype selection candidates and make rapid cycle selections in the breeding populations.  The utility of GBS for functional genomics and breeding in the Triticeae will increase with advancements in the reference genome sequence and sequencing technology.  We are currently using the GBS maps to anchor genomic sequence from whole-genome shotgun assemblies and BAC-ends.  Anchoring of the GBS tags to the reference genome will provide an additional layer of genomic information, enabling identification of more polymorphisms.  Improvements in sequencing technology will allow higher levels of multiplexing, driving per sample costs lower, further increasing the utility of this approach for genomics assisted breeding.