title: A reference genome for common bean and genome-wide analysis of dual domestications.
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.
authors.affiliation: 1] US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. [2] HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA. [3].
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.affiliation: 1] Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA. [2].
authors.forename: Phillip E
authors.initials: PE
authors.lastname: McClean
authors.affiliation: Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA.
authors.forename: Sujan
authors.initials: S
authors.lastname: Mamidi
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: G Albert
authors.initials: GA
authors.lastname: Wu
authors.affiliation: Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, Iowa, USA.
authors.forename: Steven B
authors.identifier: 0000000327778034
authors.initials: SB
authors.lastname: Cannon
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
authors.forename: Jerry
authors.initials: J
authors.lastname: Jenkins
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Shengqiang
authors.initials: S
authors.lastname: Shu
authors.affiliation: Soybean Genomics and Improvement Laboratory, US Department of Agriculture-Agricultural Research Service, Beltsville, Maryland, USA.
authors.forename: Qijian
authors.initials: Q
authors.lastname: Song
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
authors.forename: Carolina
authors.initials: C
authors.lastname: Chavarro
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
authors.forename: Mirayda
authors.initials: M
authors.lastname: Torres-Torres
authors.affiliation: 1] CNRS, Université Paris-Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France. [2] Institut National de la Recherche Agronomique (INRA), Université Paris-Sud, Unité Mixte de Recherche de Génétique Végétale, Gif-sur-Yvette, France.
authors.forename: Valerie
authors.initials: V
authors.lastname: Geffroy
authors.affiliation: Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA.
authors.forename: Samira Mafi
authors.initials: SM
authors.lastname: Moghaddam
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
authors.forename: Dongying
authors.initials: D
authors.lastname: Gao
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
authors.forename: Brian
authors.initials: B
authors.lastname: Abernathy
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Kerrie
authors.initials: K
authors.lastname: Barry
authors.affiliation: Department of Agricultural and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Blair
authors.affiliation: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Brick
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Mansi
authors.initials: M
authors.lastname: Chovatia
authors.affiliation: Department of Plant Sciences, University of California, Davis, Davis, California, USA.
authors.forename: Paul
authors.identifier: 0000000210564665
authors.initials: P
authors.lastname: Gepts
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Goodstein
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Gonzales
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Uffe
authors.initials: U
authors.lastname: Hellsten
authors.affiliation: 1] Soybean Genomics and Improvement Laboratory, US Department of Agriculture-Agricultural Research Service, Beltsville, Maryland, USA. [2].
authors.forename: David L
authors.initials: DL
authors.lastname: Hyten
authors.affiliation: Soybean Genomics and Improvement Laboratory, US Department of Agriculture-Agricultural Research Service, Beltsville, Maryland, USA.
authors.forename: Gaofeng
authors.initials: G
authors.lastname: Jia
authors.affiliation: Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.
authors.forename: James D
authors.initials: JD
authors.lastname: Kelly
authors.affiliation: Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USA.
authors.forename: Dave
authors.initials: D
authors.lastname: Kudrna
authors.affiliation: Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA.
authors.forename: Rian
authors.initials: R
authors.lastname: Lee
authors.affiliation: CNRS, Université Paris-Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France.
authors.forename: Manon M S
authors.initials: MM
authors.lastname: Richard
authors.affiliation: Vegetable and Forage Crop Research Unit, US Department of Agriculture-Agricultural Research Service, Prosser, Washington, USA.
authors.forename: Phillip N
authors.initials: PN
authors.lastname: Miklas
authors.affiliation: Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA.
authors.forename: Juan M
authors.initials: JM
authors.lastname: Osorno
authors.affiliation: 1] Soybean Genomics and Improvement Laboratory, US Department of Agriculture-Agricultural Research Service, Beltsville, Maryland, USA. [2].
authors.forename: Josiane
authors.initials: J
authors.lastname: Rodrigues
authors.affiliation: CNRS, Université Paris-Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Thareau
authors.affiliation: Panhandle Research and Extension Center, University of Nebraska, Scottsbluff, Nebraska, USA.
authors.forename: Carlos A
authors.initials: CA
authors.lastname: Urrea
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Mei
authors.initials: M
authors.lastname: Wang
authors.affiliation: Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USA.
authors.forename: Yeisoo
authors.initials: Y
authors.lastname: Yu
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Ming
authors.initials: M
authors.lastname: Zhang
authors.affiliation: Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USA.
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.affiliation: Soybean Genomics and Improvement Laboratory, US Department of Agriculture-Agricultural Research Service, Beltsville, Maryland, USA.
authors.forename: Perry B
authors.initials: PB
authors.lastname: Cregan
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Rokhsar
authors.affiliation: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Jackson
mesh_terms: D002489:Central America; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D018556:Crops, Agricultural / Q000235:genetics* / Q000254:growth & development; D017343:Genes, Plant; D018745:Genome, Plant; D006801:Humans; D008969:Molecular Sequence Data; D027805:Phaseolus / Q000235:genetics* / Q000254:growth & development; D018515:Plant Leaves / Q000737:chemistry / Q000235:genetics; D011003:Ploidies; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci; D012015:Reference Standards; D012639:Seeds / Q000737:chemistry / Q000235:genetics; D017422:Sequence Analysis, DNA; D013020:South America