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

M. Jayakodi; S. Padmarasu; G. Haberer; V.S. Bonthala; H. Gundlach; C. Monat; T. Lux; N. Kamal; D. Lang; A. Himmelbach; J. Ens; X-Q Zhang; T.T. Angessa; G. Zhou; C. Tan; C. Hill; P. Wang; M. Schreiber; L.B. Boston; C. Plott; J. Jenkins; Y. Guo; A. Fiebig; H. Budak; D. Xu; J. Zhang; C. Wang; J. Grimwood; J. Schmutz; G. Guo; G. Zhang; K. Mochida; T. Hirayama; K. Sato; K.J. Chalmers; P. Langridge; R. Waugh; C.J. Pozniak; U. Scholz; K.F.X. Mayer; M. Spannagl; C. Li; M. Mascher; N. Stein

doi:10.1038/s41586-020-2947-8

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

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

M. Jayakodi, S. Padmarasu, G. Haberer, V.S. Bonthala, H. Gundlach, C. Monat, T. Lux, N. Kamal, D. Lang, A. Himmelbach, …

Nature, Vol.588, pp.284-289

2020

DOI: https://doi.org/10.1038/s41586-020-2947-8

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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.

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Title: The barley pan-genome reveals the hidden legacy of mutation breeding
Authors/Creators: M. Jayakodi (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
S. Padmarasu (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
G. Haberer (Author/Creator) - Plant (United States)
V.S. Bonthala (Author/Creator) - Plant (United States)
H. Gundlach (Author/Creator) - Plant (United States)
C. Monat (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
T. Lux (Author/Creator) - Plant (United States)
N. Kamal (Author/Creator) - Plant (United States)
D. Lang (Author/Creator) - Plant (United States)
A. Himmelbach (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
J. Ens (Author/Creator) - University of Saskatchewan
X-Q Zhang (Author/Creator) - Murdoch University
T.T. Angessa (Author/Creator) - Murdoch University
G. Zhou (Author/Creator) - Department of Primary Industries and Regional Development
C. Tan (Author/Creator) - Murdoch University
C. Hill (Author/Creator) - Murdoch University
P. Wang (Author/Creator) - Murdoch University
M. Schreiber (Author/Creator) - James Hutton Institute
L.B. Boston (Author/Creator) - HudsonAlpha Institute for Biotechnology
C. Plott (Author/Creator) - HudsonAlpha Institute for Biotechnology
J. Jenkins (Author/Creator)
Y. Guo (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
A. Fiebig (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
H. Budak (Author/Creator) - Montana BioAg Inc, Missoula, MT, USA.
D. Xu (Author/Creator) - Institute of Crop Sciences
J. Zhang (Author/Creator) - Institute of Crop Sciences
C. Wang (Author/Creator) - Institute of Crop Sciences
J. Grimwood (Author/Creator) - HudsonAlpha Institute for Biotechnology
J. Schmutz (Author/Creator) - HudsonAlpha Institute for Biotechnology
G. Guo (Author/Creator) - Institute of Crop Sciences
G. Zhang (Author/Creator) - Zhejiang University
K. Mochida (Author/Creator) - Okayama University
T. Hirayama (Author/Creator) - Okayama University
K. Sato (Author/Creator) - Okayama University
K.J. Chalmers (Author/Creator) - The University of Adelaide
P. Langridge (Author/Creator) - The University of Adelaide
R. Waugh (Author/Creator) - The University of Adelaide
C.J. Pozniak (Author/Creator) - University of Saskatchewan
U. Scholz (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
K.F.X. Mayer (Author/Creator) - Technical University of Munich
M. Spannagl (Author/Creator) - Plant (United States)
C. Li (Author/Creator) - Department of Primary Industries and Regional Development
M. Mascher (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
N. Stein (Author/Creator) - Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK)
Publication Details: Nature, Vol.588, pp.284-289
Publisher: Nature Publishing Group
Identifiers: 991005540801607891
Copyright: © 2020 The Authors.
Murdoch Affiliation: State Agricultural Biotechnology Centre; Western Barley Genetics Alliance; School of Agricultural Sciences
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Biotechnology & Applied Microbiology
ESI research areas: Molecular Biology & Genetics