Utilization of IWGSC Wheat Sequence Resources: Application to Wheat Breeding

In recent years there has been an explosion of genomic information available to the wheat community, including the availability of millions of new single nucleotide polymorphism (SNP) markers, and the compilation of assembled wheat genome sequence information. However, a significant challenge still remains in the application and deployment of these resources to practical plant breeding and cultivar development.  In our breeding programs, we have utilized the wheat survey sequence released by the International Wheat Genome Sequencing Consortium (IWGSC) to anchor existing low throughput DNA markers already deployed by wheat breeders.  This allowed discovery of improved SNP markers better suited to high throughput marker-assisted selection platforms.  In addition, we have used the survey sequence as a "pseudo-reference"  for anchoring of short reads from genotype x sequence, exome, and shot-gun sequencing experiments for variant discovery and high density mapping of high-priority traits targeted by our wheat breeding programs.  In addition to the IWGSC survey sequence, we have coupled exome sequencing of diversity panels with the completed reference sequence of chromosome 3B to quickly identify focused genomic regions and candidate genes that influence phenotypic expression of insect resistance.  The DNA markers from these experiments have been validated in our both our hexaploid and tetraploid wheat breeding programs, and to date, none have shown ascertainment bias.  These results show immediate utility of a high quality reference sequence of the wheat genome for targeted marker discovery for wheat breeding and supports the need for continued efforts to develop a genome sequence that is anchored to genetic-phenotypic maps.