A reference genome for common bean and genome-wide analysis of dual domestications

Authors

• Jeremy Schmutz, US Department of Energy Joint Genome Institute, Walnut Creek, California
• Phillip E. McClean, North Dakota State UniversityFollow
• Sujan Mamidi, North Dakota State University
• G. Albert Wu, US Department of Energy Joint Genome Institute, Walnut Creek, California
• Steven B. Cannon, 4Corn Insects and Crop Genetics Research Unit, US Department of Agriculture–Agricultural Research Service, Ames, Iowa
• Jane Grimwood, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
• Jerry Jenkins, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama
• Shengqiang Shu, US Department of Energy Joint Genome Institute, Walnut Creek, California
• Qijian Song, Soybean Genomics and Improvement Laboratory, USAD-ARSFollow
• Carolina Chavarro, University of Georgia
• Mirayda Torres-Torres, University of Georgia
• Valerie Geffroy, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
• Samira Mafi Moghaddam, North Dakota State University
• Dongying Gao, University of Georgia
• Brian Abernathy, University of Georgia
• Kerrie Barry, US Department of Energy Joint Genome Institute, Walnut Creek, California
• Matthew Blair, Tennessee State University
• Mark A. Brick, Colorado State UniversityFollow
• Mansi Chovatia, US Department of Energy Joint Genome Institute, Walnut Creek, California
• Paul Gepts, University of California
• David M. Goodstein, US Department of Energy Joint Genome Institute, Walnut Creek, California
• Michael Gonzales, University of Georgia
• Uffe Hellsten, US Department of Energy Joint Genome Institute, Walnut Creek, California
• D. L. Hyten, USDA-ARS, Soybean Genomics and Improvement Laboratory, Beltsville, MarylandFollow
• Gaofeng Jia, Soybean Genomics and Improvement Laboratory, US Department of Agriculture–Agricultural Research Service, Beltsville, Maryland
• James D. Kelly, Michigan State University
• Dave Kudrna, University of Arizona
• Rian Lee, North Dakota State UniversityFollow
• Manon M.S. Richard, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
• Phillip N. Miklas, Vegetable and Forage Crop Research Unit, US Department of Agriculture–Agricultural Research Service, Prosser, Washington
• Juan M. Osorno, North Dakota State UniversityFollow
• Josiane Rodrigues, Soybean Genomics and Improvement Laboratory, US Department of Agriculture–Agricultural Research Service, Beltsville, Maryland
• Vincent Thareau, Université Paris–Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France
• Carlos A. Urrea Florez, University of Nebraska-LincolnFollow
• Mei Wang, US Department of Energy Joint Genome Institute, Walnut Creek, California
• Yeisoo Yu, University of Arizona
• Ming Zhang, US Department of Energy Joint Genome Institute, Walnut Creek, California
• Rod A. Wing, University of Arizona
• P. B. Cregan, USDA-ARS, Soybean Genomics and Improvement Lab., Beltsville, MarylandFollow
• Daniel S. Rokhsar, US Department of Energy Joint Genome Institute, Walnut Creek, California
• Scott A. Jackson, University of Georgia

ORCID IDs

D. L. Hyten

Document Type

Article

Date of this Version

2014

Citation

Nature Genetics, Volume 46, Number 7. July 2014

Abstract

Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.