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

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

Nature 588, 284-289 (2020)
Publ. Version/Full Text DOI PMC
Open Access Hybrid
Creative Commons Lizenzvertrag
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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Publication type Article: Journal article
Document type Scientific Article
Keywords Association; Sequence; Framework; Adaptation; Diversity; Capture; Length; Model; Tool
ISSN (print) / ISBN 0028-0836
e-ISSN 1476-4687
Journal Nature
Quellenangaben Volume: 588, Issue: 7837, Pages: 284-289 Article Number: , Supplement: ,
Publisher Nature Publishing Group
Publishing Place London
Reviewing status Peer reviewed
Institute(s) Research Unit Plant Genome and Systems Biology (PGSB)
Grants European Research Council (ERC Shuffle)
Australian Grain Research and Development Cooperation
JST CREST Japan
JST Mirai Program Japan
National Key R&D Program of China
China Agriculture Research System
Agricultural Science and Technology Innovation Program
Genome Canada
Genome Prairie
Natural Science Foundation of China
German Federal Ministry of Education and Research