Pan-genomic studies aim at representing the entire sequence diversity within a species to provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Cost reductions in high-throughput sequencing and advances in sequence assembly algorithms have made it possible to create multiple reference genome sequences along with a catalogue of all forms of genetic variations in plant species with large and complex or polyploid genomes. In this talk, we will summarize our work in barley pan-genomics: the selection of representative core sets by genebank genomics, the assembly of chromosome-scale reference sequences, and the discovery of structural variants associated with agronomic traits. A future challenge will be the development of pan-genome interfaces for easy access by breeders and geneticists.
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