The Newest Tool-Kit for Mapping, Cloning and Sequencing in Barley and Beyond

Barley (Hordeum vulgare L.) is an important cereal crop that is used for human and animal nutrition and serves as a model organism for the genetics of other Triticeae such as wheat and rye. A physical map integrated with various genetic maps, BAC survey sequence data, a whole-genome shotgun (WGS) and ~26,000 high-confidence gene models is available to the research community. The genetic anchoring of both the WGS assembly and the physical map was recently improved substantially by ultra-dense genotyping of two genetic mapping populations by next-generation sequencing. In this talk, we will illustrate how these comprehensive genomic resources in conjunction with state-of-the-art technologies such as Illumina and IonTorrent sequencing and computational analysis pipelines can be leveraged to expedite mapping and cloning in barley and related species. Two strategies for cost-efficient reduced-representation resequencing of the complex 5 Gb barley genome have been developed recently. Exome capture uses oligonucleotide baits to enrich mRNA-coding exons for selective deep-coverage resequencing and subsequent high-quality variant discovery. Genotyping-by-sequencing (GBS) employs restriction enzyme digestion together with multiplexed next-generation sequencing for high-throughput and high-density genotyping of mapping populations and diversity panels. The current sequence-enriched physical and genetic framework of barley is able to contextualize the sequence variants discovered by reduced-representation resequencing and enables reference-based genetic mapping. We will report about applications of exome sequencing and GBS to fine-mapping of phenotypic traits in bi-parental mapping populations, to the delineation of chromosomal segments introgressed from exotic germplasm with high precision, and to the unbiased study of phylogenetic distance between various accessions of cultivated barley and its wild relatives.