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The barley pan-genome reveals the hidden legacy of mutation breeding

  Murukarthick Jayakodi, Sudharsan Padmarasu, Georg Haberer, Venkata Suresh Bonthala, Heidrun Gundlach, Cécile Monat, Thomas Lux, Nadia Kamal, Daniel Lang, Axel Himmelbach, Jennifer Ens, Xiao-Qi Zhang, Tefera T. Angessa, Gaofeng Zhou, Cong Tan, Camilla Hill, Penghao Wang, Miriam Schreiber, Lori B. Boston, Christopher Plott, Jerry Jenkins, Yu Guo, Anne Fiebig, Hikmet Budak, Dongdong Xu, Jing Zhang, Chunchao Wang, Jane Grimwood, Jeremy Schmutz, Ganggang Guo, Guoping Zhang, Keiichi Mochida, Takashi Hirayama, Kazuhiro Sato, Kenneth J. Chalmers, Peter Langridge, Robbie Waugh, Curtis J. Pozniak, Uwe Scholz, Klaus F. X. Mayer, Manuel Spannagl, Nils Stein

  Nature, 25 November 2020, IF: 42.778 doi: 10.1038/s41586-020-2947-8


  Genetic diversity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence diversity of a crop species (known as the ‘pan-genome’1). 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 that is adapted to a wide range of agro-climatic conditions2. Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley—comprising landraces, cultivars and a wild barley—that were selected as representatives of global barley diversity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm; one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.