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


Jeremy Schmutz Phillip E McClean Sujan Mamidi G Albert Wu Steven B Cannon Jane Grimwood Jerry Jenkins Shengqiang Shu Qijian Song Carolina Chavarro Mirayda Torres-Torres Valerie Geffroy Samira Mafi Moghaddam Dongying Gao Brian Abernathy Kerrie Barry
Matthew Blair Mark A Brick Mansi Chovatia Paul Gepts David M Goodstein Michael Gonzales Uffe Hellsten David L Hyten Gaofeng Jia James D Kelly Dave Kudrna Rian Lee Manon M S Richard Phillip N Miklas Juan M Osorno Josiane Rodrigues Vincent Thareau
Carlos A Urrea Mei Wang Yeisoo Yu Ming Zhang Rod A Wing Perry B Cregan Daniel S Rokhsar Scott A Jackson

Nature Genetics (2014) doi:10.1038/ng.3008

Received 08 November 2013, Accepted 15 May 2014, Published online 08 June 2014



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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