Barley Pan-Genome analysis (SHAPE Project)

Genetic diversity is key to crop improvement. Due to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (the “pan-genome”). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley (Hordeum vulgare L.) is an important cereal crop with a long history of cultivation and adapted to a wide range of agro-climatic conditions. Here, we report the construction of chromosome-scale sequence assemblies for 20 barley genotypes, comprising landraces, cultivars and one wild barley selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis with whole-genome shotgun sequence of 300 genebank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions frequent in current elite barley germplasm; one likely the product of mutation breeding and the other tightly linked to a locus involved in geographic range expansion. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.