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.

Agriculture Victoria AgriBio Centre for AgriBioscience Bundoora Victoria Australia

Agroécologie INRAE Institut Agro University Bourgogne University Bourgogne Franche Comté Dijon France

Bingen Technical University of Applied Sciences Bingen Germany

Biology Centre Czech Academy of Sciences Institute of Plant Molecular Biology České Budějovice Czech Republic

Center for Quantitative Genetics and Genomics Aarhus University Aarhus C Denmark

Center of Integrated Breeding Research Georg August University Göttingen Germany

Department of Agricultural Sciences University of Helsinki Helsinki Finland

Department of Analytical Chemistry Faculty of Science Palacky University Olomouc Czech Republic

Department of Botany Faculty of Science Palacky University Olomouc Czech Republic

Department of Molecular Biology and Genetics Aarhus University Aarhus C Denmark

Department of Plant Breeding Justus Liebig University Giessen Giessen Germany

German Centre for Integrative Biodiversity Research Halle Jena Leipzig Leipzig Germany

IBG 4 Bioinformatics Forschungszentrum Jülich Jülich Germany

Institute for Biological Data Science CEPLAS Heinrich Heine University Düsseldorf Düsseldorf Germany

Institute of Biotechnology University of Helsinki Helsinki Finland

Institute of Experimental Botany of the Czech Academy of Sciences Centre of the Region Haná for Biotechnological and Agricultural Research Olomouc Czech Republic

Instituto Andaluz de Investigación y Formación Agraria Pesquera Alimentaria y de la Producción Ecológica Área de Mejora y Biotecnología Centro Alameda del Obispo Córdoba Spain

KeyGene Wageningen The Netherlands

Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben Seeland Germany

Natural Resources Institute Finland Helsinki Finland

Nordic Seed Odder Denmark

Plant Genome and Systems Biology Helmholtz Center Munich German Research Center for Environmental Health Neuherberg Germany

School of Agriculture Policy and Development University of Reading Reading UK

Sejet Planteforædling Horsens Denmark

Viikki Plant Science Centre University of Helsinki Helsinki Finland Córdoba Spain

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Nature. 2023 Mar;615(7953):587-588. doi: 10.1038/d41586-023-00461-y. PubMed

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