A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum
2025
Feng, Jia-Wu | Pidon, Hélène | Cuacos, Maria | Lux, Thomas | Himmelbach, Axel | Haghi, Reza | Fuchs, Jörg | Haberer, Georg | Kuo, Yi-Tzu | Guo, Yu | Jayakodi, Murukarthick | Toegelová, Helena | Harpke, Dörte | Knauft, Manuela | Fiebig, Anne | Maruschewski, Maren | Ronen, Moshe | Sharon, Amir | Šimková, Hana | Mayer, Klaus, F. X. | Spannagl, Manuel | Kumlehn, Jochen | Heckmann, Stefan | Houben, Andreas | Blattner, Frank, R. | Stein, Nils | Mascher, Martin | Leibniz Institute of Plant Genetics and Crop Plant Research [Gatersleben] (IPK-Gatersleben) | Julius Kühn-Institut - Federal Research Centre for Cultivated Plants (JKI) | Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP) ; Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier ; Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM) | Helmholtz Zentrum München = German Research Center for Environmental Health (HMGU) | Texas A and M AgriLife Research ; Texas A&M University System | Tel Aviv University (TAU) | School of Plant Sciences and Food Security ; Tel Aviv University (TAU) | Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS) ; Czech Academy of Sciences [Prague] (CAS) | Centre of Plant Structural and Functional Genomics ; Institute of Experimental Botany of the Czech Academy of Sciences (IEB / CAS) ; Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS) | Technische Universität Munchen - Technical University Munich - Université Technique de Munich (TUM) | Murdoch University [Perth] | Martin-Luther-Universität Halle Wittenberg - Martin-Luther-University Halle Wittenberg (MLU) | German Centre for Integrative Biodiversity Research (iDiv) | This research was supported by IPK core funding. Genomic inquiries into barley wild relatives by M. Mascher. are supported by the European Commission (ERC Starting Grant TRANSFER 949873). M.S. and K.F.X.M. acknowledge support by the German Federal Ministry of Education and Research (BMBF) under project number 031B0190 (de.NBI). S.H. acknowledges support by the European Commission (ERC Starting Grant MEIOBARMIX 949618). M.C. acknowledges funding from the German federal state of Saxony-Anhalt (grant ZB I 180). Open access funding provided by Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK).
Data availability: All of the sequence data collected in this study have been deposited at the European Nucleotide Archive under the BioProject accession codes PRJEB65276 (genome assemblies, transcriptome Illumina data and GBS data) and PRJEB65918 (pollen nucleus single-cell sequencing data). Accession codes for individual genotypes are listed in Supplementary Tables 1, 2 and 7 (pangenome assemblies and associated raw data), Supplementary Table 6 (pollen single-nucleus sequencing data) and Supplementary Table 12 (GBS). The assemblies and annotations are available for download from https://galaxy-web.ipk-gatersleben.de/libraries/folders/Fb701da857886499b. The variant matrix and pangenome graphs are available via the Plant Genomics and Phenomics Research Data Repository120 at https://doi.org/10.5447/ipk/2025/4.Code availability: Code for genome assembly and data analysis is available at: https://github.com/jia-wu-feng/Pan_Bulbosum. Code for gene projection is available at: https://github.com/GeorgHaberer/gene_projection/tree/main/panhordeum. Code for analysis of orthologous groups is available at: https://github.com/PGSB-HMGU/hbulbosum/tree/main.
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Afficher plus [+] Moins [-]anglais. Wild plants can contribute valuable genes to their domesticated relatives. Fertility barriers and a lack of genomic resources have hindered the effective use of crop-wild introgressions. Decades of research into barley's closest wild relative, Hordeum bulbosum, a grass native to the Mediterranean basin and Western Asia, have yet to manifest themselves in the release of a cultivar bearing alien genes. Here we construct a pangenome of bulbous barley comprising 10 phased genome sequence assemblies amounting to 32 distinct haplotypes. Autotetraploid cytotypes, among which the donors of resistance-conferring introgressions are found, arose at least twice, and are connected among each other and to diploid forms through gene flow. The differential amplification of transposable elements after barley and H. bulbosum diverged from each other is responsible for genome size differences between them. We illustrate the translational value of our resource by mapping non-host resistance to a viral pathogen to a structurally diverse multigene cluster that has been implicated in diverse immune responses in wheat and barley.
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