Journal article
A reference genome for common bean and genome-wide analysis of dual domestications
Nature genetics, Vol.46(7), pp.707-713
07/2014
Handle:
https://hdl.handle.net/2376/117486
PMCID: PMC7048698
PMID: 24908249
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.
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Details
- Title
- A reference genome for common bean and genome-wide analysis of dual domestications
- Creators
- Jeremy Schmutz - 1] US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.Phillip E McClean - 1] Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA.Sujan Mamidi - Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USAG Albert Wu - US Department of Energy Joint Genome Institute, Walnut Creek, California, USASteven B Cannon - Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, Iowa, USAJane Grimwood - HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USAJerry Jenkins - HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USAShengqiang Shu - US Department of Energy Joint Genome Institute, Walnut Creek, California, USAQijian Song - Soybean Genomics and Improvement Laboratory, US Department of Agriculture-Agricultural Research Service, Beltsville, Maryland, USACarolina Chavarro - Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USAMirayda Torres-Torres - Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USAValerie Geffroy - 1] CNRS, Université Paris-Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France. Institut National de la Recherche Agronomique (INRA), Université Paris-Sud, Unité Mixte de Recherche de Génétique Végétale, Gif-sur-Yvette, FranceSamira Mafi Moghaddam - Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USADongying Gao - Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USABrian Abernathy - Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USAKerrie Barry - US Department of Energy Joint Genome Institute, Walnut Creek, California, USAMatthew Blair - Department of Agricultural and Natural Sciences, Tennessee State University, Nashville, Tennessee, USAMark A Brick - Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USAMansi Chovatia - US Department of Energy Joint Genome Institute, Walnut Creek, California, USAPaul Gepts - Department of Plant Sciences, University of California, Davis, Davis, California, USADavid M Goodstein - US Department of Energy Joint Genome Institute, Walnut Creek, California, USAMichael Gonzales - Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USAUffe Hellsten - US Department of Energy Joint Genome Institute, Walnut Creek, California, USADavid L Hyten - 1] Soybean Genomics and Improvement Laboratory, US Department of Agriculture-Agricultural Research Service, Beltsville, Maryland, USA.Gaofeng Jia - Soybean Genomics and Improvement Laboratory, US Department of Agriculture-Agricultural Research Service, Beltsville, Maryland, USAJames D Kelly - Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USADave Kudrna - Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USARian Lee - Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USAManon M S Richard - CNRS, Université Paris-Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, FrancePhillip N Miklas - Vegetable and Forage Crop Research Unit, US Department of Agriculture-Agricultural Research Service, Prosser, Washington, USAJuan M Osorno - Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USAJosiane Rodrigues - 1] Soybean Genomics and Improvement Laboratory, US Department of Agriculture-Agricultural Research Service, Beltsville, Maryland, USA.Vincent Thareau - CNRS, Université Paris-Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, FranceCarlos A Urrea - Panhandle Research and Extension Center, University of Nebraska, Scottsbluff, Nebraska, USAMei Wang - US Department of Energy Joint Genome Institute, Walnut Creek, California, USAYeisoo Yu - Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USAMing Zhang - US Department of Energy Joint Genome Institute, Walnut Creek, California, USARod A Wing - Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USAPerry B Cregan - Soybean Genomics and Improvement Laboratory, US Department of Agriculture-Agricultural Research Service, Beltsville, Maryland, USADaniel S Rokhsar - US Department of Energy Joint Genome Institute, Walnut Creek, California, USAScott A Jackson - Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA
- Publication Details
- Nature genetics, Vol.46(7), pp.707-713
- Academic Unit
- Crop and Soil Sciences, Department of; Plant Pathology, Department of
- Publisher
- United States
- Identifiers
- 99900547988101842
- Language
- English
- Resource Type
- Journal article