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Nat Genet. 2014 Jul;46(7):707-13. doi: 10.1038/ng.3008. Epub 2014 Jun 8.

A reference genome for common bean and genome-wide analysis of dual domestications.

Author information

1
1] US Department of Energy Joint Genome Institute, Walnut Creek, California, USA. [2] HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA. [3].
2
1] Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA. [2].
3
Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA.
4
US Department of Energy Joint Genome Institute, Walnut Creek, California, USA.
5
Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, Iowa, USA.
6
HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.
7
Soybean Genomics and Improvement Laboratory, US Department of Agriculture-Agricultural Research Service, Beltsville, Maryland, USA.
8
Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, USA.
9
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.
10
Department of Agricultural and Natural Sciences, Tennessee State University, Nashville, Tennessee, USA.
11
Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, USA.
12
Department of Plant Sciences, University of California, Davis, Davis, California, USA.
13
1] Soybean Genomics and Improvement Laboratory, US Department of Agriculture-Agricultural Research Service, Beltsville, Maryland, USA. [2].
14
Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, USA.
15
Arizona Genomics Institute, University of Arizona, Tucson, Arizona, USA.
16
CNRS, Université Paris-Sud, Institut de Biologie des Plantes, UMR 8618, Saclay Plant Sciences (SPS), Orsay, France.
17
Vegetable and Forage Crop Research Unit, US Department of Agriculture-Agricultural Research Service, Prosser, Washington, USA.
18
Panhandle Research and Extension Center, University of Nebraska, Scottsbluff, Nebraska, USA.

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.

PMID:
24908249
DOI:
10.1038/ng.3008
[Indexed for MEDLINE]
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