Agronomy and Horticulture Department

 

Authors

Jeremy Schmutz, US Department of Energy Joint Genome Institute, Walnut Creek, California
Phillip E. McClean, North Dakota State University
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 University
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 University
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 University
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

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.