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, Chengdao Li (), Martin Mascher () and Nils Stein ()
Additional contact information
Murukarthick Jayakodi: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Sudharsan Padmarasu: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Georg Haberer: German Research Center for Environmental Health
Venkata Suresh Bonthala: German Research Center for Environmental Health
Heidrun Gundlach: German Research Center for Environmental Health
Cécile Monat: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Thomas Lux: German Research Center for Environmental Health
Nadia Kamal: German Research Center for Environmental Health
Daniel Lang: German Research Center for Environmental Health
Axel Himmelbach: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Jennifer Ens: University of Saskatchewan
Xiao-Qi Zhang: Murdoch University
Tefera T. Angessa: Murdoch University
Gaofeng Zhou: Murdoch University
Cong Tan: Murdoch University
Camilla Hill: Murdoch University
Penghao Wang: Murdoch University
Miriam Schreiber: The James Hutton Institute
Lori B. Boston: HudsonAlpha, Institute for Biotechnology
Christopher Plott: HudsonAlpha, Institute for Biotechnology
Jerry Jenkins: HudsonAlpha, Institute for Biotechnology
Yu Guo: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Anne Fiebig: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Hikmet Budak: Montana BioAg Inc
Dongdong Xu: Chinese Academy of Agricultural Sciences (ICS-CAAS)
Jing Zhang: Chinese Academy of Agricultural Sciences (ICS-CAAS)
Chunchao Wang: Chinese Academy of Agricultural Sciences (ICS-CAAS)
Jane Grimwood: HudsonAlpha, Institute for Biotechnology
Jeremy Schmutz: HudsonAlpha, Institute for Biotechnology
Ganggang Guo: Chinese Academy of Agricultural Sciences (ICS-CAAS)
Guoping Zhang: Zhejiang University
Keiichi Mochida: Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science
Takashi Hirayama: Okayama University
Kazuhiro Sato: Okayama University
Kenneth J. Chalmers: University of Adelaide
Peter Langridge: University of Adelaide
Robbie Waugh: The James Hutton Institute
Curtis J. Pozniak: University of Saskatchewan
Uwe Scholz: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Klaus F. X. Mayer: German Research Center for Environmental Health
Manuel Spannagl: German Research Center for Environmental Health
Chengdao Li: Murdoch University
Martin Mascher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Nils Stein: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben

Nature, 2020, vol. 588, issue 7837, 284-289

Abstract: Abstract 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.

Date: 2020
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DOI: 10.1038/s41586-020-2947-8

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