1. A reference genome for common bean and genome-wide analysis of dual domestications
- Author
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Jane Grimwood, Kerrie Barry, Gaofeng Jia, Paul Gepts, Brian Abernathy, Mirayda Torres-Torres, Mansi Chovatia, Ming Zhang, Manon M.S. Richard, Mark A. Brick, Phillip E. McClean, Samira Mafi Moghaddam, Mei Wang, Valérie Geffroy, Steven B. Cannon, Carolina Chavarro, David L. Hyten, Dongying Gao, Qijian Song, Daniel S. Rokhsar, G Albert Wu, Shengqiang Shu, Scott A. Jackson, Jerry Jenkins, Dave Kudrna, Matthew W. Blair, Phillip N. Miklas, Vincent Thareau, Rod A. Wing, Michael D. Gonzales, Carlos A. Urrea, Sujan Mamidi, Yeisoo Yu, Juan M. Osorno, Uffe Hellsten, James D. Kelly, Rian Lee, Jeremy Schmutz, David Goodstein, Josiane Rodrigues, Perry B. Cregan, 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), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), 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), University of California [Davis] (UC Davis), University of California-University of California, 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], Schmutz, Jeremy, and McClean, Phillip E.
- Subjects
0106 biological sciences ,[SDV]Life Sciences [q-bio] ,Medical and Health Sciences ,01 natural sciences ,Genome ,2. Zero hunger ,Genetics ,Phaseolus ,0303 health sciences ,Chromosome Mapping ,food and beverages ,Single Nucleotide ,Biological Sciences ,Reference Standards ,Seeds ,Gene pool ,Sequence Analysis ,Genome, Plant ,Crops, Agricultural ,Plant genetics ,Sequence analysis ,Molecular Sequence Data ,Quantitative Trait Loci ,Crops ,Quantitative trait locus ,Biology ,Genes, Plant ,Polymorphism, Single Nucleotide ,Article ,Chromosomes ,Chromosomes, Plant ,03 medical and health sciences ,domestication ,Humans ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Polymorphism ,soja ,Domestication ,Gene ,030304 developmental biology ,Agricultural ,Ploidies ,génome ,Human Genome ,Central America ,phaseolus vulgaris ,Plant ,DNA ,Sequence Analysis, DNA ,haricot commun ,South America ,biology.organism_classification ,Plant Leaves ,Genes ,Developmental Biology ,010606 plant biology & botany ,Reference genome - Abstract
Scott Jackson, Jeremy Schmutz, Phillip McClean and colleagues report the genome sequence of the common bean (Phaseolus vulgaris) and resequenced wild individuals and landraces from Mesoamerican and Andean gene pools, showing that common bean underwent two independent domestications. Supplementary information The online version of this article (doi:10.1038/ng.3008) contains supplementary material, which is available to authorized users., 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. Supplementary information The online version of this article (doi:10.1038/ng.3008) contains supplementary material, which is available to authorized users.
- Published
- 2014