The barley pan-genome reveals the hidden legacy of mutation breeding
Open accessAbstract
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 conditions 2 . 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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The availability of barley pan-genome sequences facilitates the identification of structural variations and conserved sequences within the genes of interest and pinpoints the most plausible gene for editing.
“Furthermore, the availability of barley pan-genome sequences facilitates the identification of structural variations and conserved sequences within the genes of interest and pinpoints the most plausible gene for editing (Jayakodi et al., 2020).”
From Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance (2023) · cites this paper as Jayakodi et al., 2020
The transformation capacity of pan-genome accessions is yet to be tested.
“A barley pan-genome is now available that provides more sequence information for gene editing, but the transformation capacity of pan-genome accessions is yet to be tested (Jayakodi et al., 2020).”
From Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance (2023) · cites this paper as Jayakodi et al., 2020
A barley pan-genome is now available that provides more sequence information for gene editing.
“A barley pan-genome is now available that provides more sequence information for gene editing, but the transformation capacity of pan-genome accessions is yet to be tested (Jayakodi et al., 2020).”
From Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance (2023) · cites this paper as Jayakodi et al., 2020
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- [43]Padmarasu, S., Himmelbach, A., Mascher, M. & Stein, N. in Plant Long Non-Coding RNAs (eds Chekanova, J. & Wang, H.-L.) 441–472 (Springer, 2019).
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“A barley pan-genome is now available that provides more sequence information for gene editing, but the transformation capacity of pan-genome accessions is yet to be tested (Jayakodi et al., 2020).”
Self-citation
- Authors
- Jayakodi, M., Padmarasu, S., Haberer, G., Bonthala, V. S., 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.
- Affiliations
- Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) (DE)
- Helmholtz Munich (DE)
- University of Saskatchewan (CA)
- Murdoch University (AU)
- James Hutton Institute (GB)
- HudsonAlpha Institute for Biotechnology (US)
- Chinese Academy of Agricultural Sciences (CN)
- Zhejiang University (CN)
- Kihara Institute for Biological Research (JP)
- Institute of Plant Science and Resources, Okayama University (JP)
- The University of Adelaide (AU)
- German Centre for Integrative Biodiversity Research (DE)
- Corresponding author
- Li, Chengdao
- Mascher, Martin
- Stein, Nils
- ORCID
- Jayakodi, Murukarthick
- Padmarasu, Sudharsan
- Haberer, Georg
- Bonthala, Venkata Suresh
- Gundlach, Heidrun
- Monat, Cécile
- Lux, Thomas
- Kamal, Nadia
- Lang, Daniel
- Himmelbach, Axel
- Ens, Jennifer
- Zhang, Xiao-Qi
- Angessa, Tefera T.
- Zhou, Gaofeng
- Tan, Cong
- Hill, Camilla
- Wang, Penghao
- Schreiber, Miriam
- Boston, Lori B.
- Plott, Christopher
- Jenkins, Jerry
- Guo, Yu
- Fiebig, Anne
- Budak, Hikmet
- Xu, Dongdong
- Zhang, Jing
- Wang, Chunchao
- Grimwood, Jane
- Schmutz, Jeremy
- Guo, Ganggang
- Zhang, Guoping
- Mochida, Keiichi
- Hirayama, Takashi
- Sato, Kazuhiro
- Chalmers, Kenneth J.
- Langridge, Peter
- Waugh, Robbie
- Pozniak, Curtis J.
- Scholz, Uwe
- Mayer, Klaus F. X.
- Spannagl, Manuel
- Li, Chengdao
- Mascher, Martin
- Stein, Nils
- Venue
- Nature
- Published
- 2020-11-25
- Volume
- 588
- Issue
- 7837
- Pages
- 284-289
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC7759462
- OpenAlex
- W3110395203
- Cited by
- 565
- References
- 65
- Citations by year
- 2026: 68 · 2025: 83 · 2024: 106 · 2023: 109 · 2022: 120 · 2021: 77 · 2020: 2
- FWCI
- 50.37
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, other-oa)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Discovery Research Portal (University of Dundee) (publishedVersion, cc-by)
- Murdoch University Research Portal (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- Site cant be reached (submittedVersion, cc-by)
- GoeScholar The Publication Server of the Georg-August-Universität Göttingen (Georg-August-Universität Göttingen) (submittedVersion, cc-by)
- PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion, cc-by)
- Funders
- Genome Canada
- National Natural Science Foundation of China (31620103912, 2018YFD1000701, CARS-05, 2018YFD1000700)
- Bundesministerium für Bildung und Forschung (031B0190)
- Genome Prairie
- German Network for Bioinformatics Infrastructure (FKZ 031A536)
- Biotechnology and Biological Sciences Research Council (BB/I00663X/1)
- Agricultural Science and Technology Innovation Program
- Core Research for Evolutional Science and Technology (JPMJCR16O4)
- JST-Mirai Program (18076896)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Wheat and Barley Genetics and Pathology
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Genetic and Environmental Crop Studies
- Keywords
- barley, pan-genome, mutation breeding, structural variants, inversion, chromosome-level genome assembly, landraces, wild barley, germplasm diversity, quantitative genetics, geographical range expansion
- MeSH terms
- Seed Bank, Plant Breeding, Whole Genome Sequencing, Hordeum, Chromosome Mapping, Genotype, Chromosome Inversion, Mutation, Polymorphism, Genetic, Reference Standards, Genome, Plant, Chromosomes, Plant, Internationality, Genetic Loci, Sequence Inversion
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