A reference genome for common bean and genome-wide analysis of dual domestications
2014
Schmutz, Jeremy | Mcclean, Phillip E. | Mamidi, Sujan | Wu, G. Albert | Cannon, Steven B. | Grimwood, Jane | Jenkins, Jerry | Shu, Shengqiang | Song, Qijian | Chavarro, Carolina | Torres-Torres, Mirayda | Geffroy, Valérie | Moghaddam, Samira Mafi | Gao, Dongying | Abernathy, Brian | Barry, Kerrie | Blair, Matthew | Brick, Mark A. | Chovatia, Mansi | Gepts, Paul | Goodstein, David M. | Gonzales, Michael | Hellsten, Uffe | Hyten, David L. | Jia, Gaofeng | Kelly, James D. | Kudrna, Dave | Lee, Rian | Richard, Manon M. S. | Miklas, Phillip N. | Osorno, Juan M. | Rodrigues, Josiane | Thareau, Vincent | Urrea, Carlos A. | Wang, Mei | Yu, Yeisoo | Zhang, Ming | Wing, Rod A. | Cregan, Perry B. | Rokhsar, Daniel S. | Jackson, Scott A. | Joint Genome institute ; United States Department of Energy | Hudson Alpha Institute for Biotechnology | Department of Plant Sciences ; North Dakota State University (NDSU) | USDA-ARS : Agricultural Research Service | United States Department of Agriculture (USDA) | Center for Applied Genetic Technologies ; University of Georgia [USA] | Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon) ; Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS) | Institut de Biologie des Plantes (IBP) ; Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS) | Tennessee State University | Department of Soil and Crop Sciences [Fort Collins] ; Colorado State University [Fort Collins] (CSU) | Department of Plant Sciences ; University of California [Davis] (UC Davis) ; University of California (UC)-University of California (UC) | Michigan State University [East Lansing] ; Michigan State University System | University of Arizona | University of Nebraska ; Partenaires INRAE | Office of Science of the US Department of Energy - US Department of Agriculture National Institute for Food and Agriculture [DE-AC02-05CH11231, 2006-35300-17266]; National Science Foundation [DBI 0822258]; US Department of Agriculture Cooperative State Research, Education and Extension Service [2009-01860, 2009-01929]
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Show more [+] Less [-]English. 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.
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