The giant diploid faba genome unlocks variation in a global protein crop

Murukarthick Jayakodi, Agnieszka A. Golicz, Jonathan Kreplak, Lavinia I. Fechete, Deepti Angra, Petr Bednář, Elesandro Bornhofen, Hailin Zhang, Raphaël Boussageon, Sukhjiwan Kaur, Kwok Cheung, Jana Čížková, Heidrun Gundlach, Asis Hallab, Baptiste Imbert, Gabriel Keeble-Gagnère, Andrea Koblížková, Lucie Kobrlová, Petra Krejčí, Troels W. Mouritzen, Pavel Neumann, Marcin Nadzieja, Linda Kærgaard Nielsen, Petr Novák, Jihad Orabi, Sudharsan Padmarasu, Tom Robertson-Shersby-Harvie, Laura Ávila Robledillo, Andrea Schiemann, Jaakko Tanskanen, Petri Törönen, Ahmed O. Warsame, Alexander H. J. Wittenberg, Axel Himmelbach, Grégoire Aubert, Pierre-Emmanuel Courty, Jaroslav Doležel, Liisa U. Holm, Luc L. Janss, Hamid Khazaei, Jiří Macas, Martin Mascher, Petr Smýkal, Rod J. Snowdon, Nils Stein, Frederick L. Stoddard, Jens Stougaard, Nadim Tayeh, Ana M. Torres, Björn Usadel, Ingo Schubert, Donal Martin O’Sullivan (), Alan H. Schulman () and Stig Uggerhøj Andersen ()
Additional contact information
Murukarthick Jayakodi: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Agnieszka A. Golicz: Justus Liebig University Giessen
Jonathan Kreplak: University Bourgogne, University Bourgogne Franche-Comté
Lavinia I. Fechete: Aarhus University
Deepti Angra: School of Agriculture, Policy and Development, University of Reading
Petr Bednář: Palacky University
Elesandro Bornhofen: Aarhus University
Hailin Zhang: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Raphaël Boussageon: University Bourgogne, University Bourgogne Franche-Comté
Sukhjiwan Kaur: Agriculture Victoria, AgriBio, Centre for AgriBioscience
Kwok Cheung: School of Agriculture, Policy and Development, University of Reading
Jana Čížková: Centre of the Region Haná for Biotechnological and Agricultural Research
Heidrun Gundlach: German Research Center for Environmental Health
Asis Hallab: IBG-4 Bioinformatics Forschungszentrum Jülich
Baptiste Imbert: University Bourgogne, University Bourgogne Franche-Comté
Gabriel Keeble-Gagnère: Agriculture Victoria, AgriBio, Centre for AgriBioscience
Andrea Koblížková: Institute of Plant Molecular Biology
Lucie Kobrlová: Palacky University
Petra Krejčí: Palacky University
Troels W. Mouritzen: Aarhus University
Pavel Neumann: Institute of Plant Molecular Biology
Marcin Nadzieja: Aarhus University
Linda Kærgaard Nielsen: Sejet Planteforædling
Petr Novák: Institute of Plant Molecular Biology
Jihad Orabi: Nordic Seed
Sudharsan Padmarasu: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Tom Robertson-Shersby-Harvie: School of Agriculture, Policy and Development, University of Reading
Laura Ávila Robledillo: Institute of Plant Molecular Biology
Andrea Schiemann: Nordic Seed
Jaakko Tanskanen: Natural Resources Institute Finland (Luke)
Petri Törönen: University of Helsinki
Ahmed O. Warsame: School of Agriculture, Policy and Development, University of Reading
Alexander H. J. Wittenberg: KeyGene
Axel Himmelbach: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Grégoire Aubert: University Bourgogne, University Bourgogne Franche-Comté
Pierre-Emmanuel Courty: University Bourgogne, University Bourgogne Franche-Comté
Jaroslav Doležel: Centre of the Region Haná for Biotechnological and Agricultural Research
Liisa U. Holm: University of Helsinki
Luc L. Janss: Aarhus University
Hamid Khazaei: Natural Resources Institute Finland (Luke)
Jiří Macas: Institute of Plant Molecular Biology
Martin Mascher: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Petr Smýkal: Palacky University
Rod J. Snowdon: Justus Liebig University Giessen
Nils Stein: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Frederick L. Stoddard: University of Helsinki
Jens Stougaard: Aarhus University
Nadim Tayeh: University Bourgogne, University Bourgogne Franche-Comté
Ana M. Torres: Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), Área de Mejora y Biotecnología, Centro Alameda del Obispo
Björn Usadel: IBG-4 Bioinformatics Forschungszentrum Jülich
Ingo Schubert: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben
Donal Martin O’Sullivan: School of Agriculture, Policy and Development, University of Reading
Alan H. Schulman: Natural Resources Institute Finland (Luke)
Stig Uggerhøj Andersen: Aarhus University

Nature, 2023, vol. 615, issue 7953, 652-659

Abstract: Abstract Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.

Date: 2023
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DOI: 10.1038/s41586-023-05791-5

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