IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v588y2020i7837d10.1038_s41586-020-2947-8.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    Agriculture and Food, Department of Primary Industries and Regional Development)

  • 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
    Yokohama City University
    Okayama University)

  • 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
    University of Adelaide
    University of Dundee)

  • 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
    Technical University of Munich)

  • Manuel Spannagl

    (German Research Center for Environmental Health)

  • Chengdao Li

    (Murdoch University
    Agriculture and Food, Department of Primary Industries and Regional Development
    Yangtze University)

  • Martin Mascher

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
    German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig)

  • Nils Stein

    (Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
    Georg-August-University Göttingen)

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.

Suggested Citation

  • Murukarthick Jayakodi & Sudharsan Padmarasu & Georg Haberer & Venkata Suresh Bonthala & Heidrun Gundlach & Cécile Monat & Thomas Lux & Nadia Kamal & Daniel Lang & Axel Himmelbach & Jennifer Ens & Xiao, 2020. "The barley pan-genome reveals the hidden legacy of mutation breeding," Nature, Nature, vol. 588(7837), pages 284-289, December.
    • Handle: RePEc:nat:nature:v:588:y:2020:i:7837:d:10.1038_s41586-020-2947-8
    DOI: 10.1038/s41586-020-2947-8
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41586-020-2947-8
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.
    File URL: https://libkey.io/10.1038/s41586-020-2947-8?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Xiaohua Yao & Leping Su & Youhua Yao & Likun An & Yixiong Bai & Xin Li & Kunlun Wu, 2022. "Isolation, sequencing of the HvnHID gene and its role in the purple-grain colour development in Tibetan hulless barley," Czech Journal of Genetics and Plant Breeding, Czech Academy of Agricultural Sciences, vol. 58(1), pages 1-9.
    2. Carmen Escudero-Martinez & Max Coulter & Rodrigo Alegria Terrazas & Alexandre Foito & Rumana Kapadia & Laura Pietrangelo & Mauro Maver & Rajiv Sharma & Alessio Aprile & Jenny Morris & Pete E. Hedley &, 2022. "Identifying plant genes shaping microbiota composition in the barley rhizosphere," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    3. Gaia Cortinovis & Leonardo Vincenzi & Robyn Anderson & Giovanni Marturano & Jacob Ian Marsh & Philipp Emanuel Bayer & Lorenzo Rocchetti & Giulia Frascarelli & Giovanna Lanzavecchia & Alice Pieri & And, 2024. "Adaptive gene loss in the common bean pan-genome during range expansion and domestication," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    4. Linsan Liu & Sarah B. Jose & Chiara Campoli & Micha M. Bayer & Miguel A. Sánchez-Diaz & Trisha McAllister & Yichun Zhou & Mhmoud Eskan & Linda Milne & Miriam Schreiber & Thomas Batstone & Ian D. Bull , 2022. "Conserved signalling components coordinate epidermal patterning and cuticle deposition in barley," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    5. Ting Wang & Shiyao Duan & Chen Xu & Yi Wang & Xinzhong Zhang & Xuefeng Xu & Liyang Chen & Zhenhai Han & Ting Wu, 2023. "Pan-genome analysis of 13 Malus accessions reveals structural and sequence variations associated with fruit traits," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    6. Sylvain Aubry, 2023. "Genebanking plant genetic resources in the postgenomic era," Agriculture and Human Values, Springer;The Agriculture, Food, & Human Values Society (AFHVS), vol. 40(3), pages 961-971, September.
    7. Chunhong Chen & Matthias Jost & Megan A. Outram & Dorian Friendship & Jian Chen & Aihua Wang & Sambasivam Periyannan & Jan Bartoš & Kateřina Holušová & Jaroslav Doležel & Peng Zhang & Dhara Bhatt & Da, 2023. "A pathogen-induced putative NAC transcription factor mediates leaf rust resistance in barley," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    8. Hoan X. Dinh & Davinder Singh & Diana Gomez de la Cruz & Goetz Hensel & Jochen Kumlehn & Martin Mascher & Nils Stein & Dragan Perovic & Michael Ayliffe & Matthew J. Moscou & Robert F. Park & Mohammad , 2022. "The barley leaf rust resistance gene Rph3 encodes a predicted membrane protein and is induced upon infection by avirulent pathotypes of Puccinia hordei," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:588:y:2020:i:7837:d:10.1038_s41586-020-2947-8. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.