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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
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    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. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.

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