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United States Department of Agriculture

Agricultural Research Service

Research Project: Enhanced Disease and Abiotic Stress Resistance in Edible Legumes

Location: Grain Legume Genetics Physiology Research

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

item Shmutz, Jeremy -
item Mcclean, Phillip -
item Mamidi, Sujan -
item Wu, Albert -
item Cannon, Steven
item Grimwood, Jane -
item Jenkins, Jerry -
item Shu, Shenqiang -
item Song, Qijian
item Chavarro, Carolina -
item Geffroy, Valerie -
item Moghaddam, Samira -
item Dongying, Gao -
item Abernathy, Brian -
item Barry, Kerrie -
item Blair, Matthew -
item Brick, Mark -
item Chovatia, Mansi -
item Gepts, Paul -
item Goodstein, David -
item Gonzales, Michael -
item Hellsten, Uffe -
item Hyten, David
item Gaofeng, Jia -
item Kelly, Jim -
item Kudrna, Dave -
item Lee, Rian -
item Manon, Richard -
item Miklas, Phillip
item Osorno, Juan -
item Rodrigues, Josiane -
item Thareau, Vincent -
item Urrea, Carlos -
item Wang, Mei -
item Yu, Yeisoo -
item Zhang, Ming -
item Wing, Rod -
item Cregan, Perry
item Rokhsar, Daniel -
item Jackson, Scott -

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: May 13, 2014
Publication Date: June 8, 2014
Citation: Shmutz, J., Mcclean, P., Mamidi, S., Wu, A., Cannon, S.B., Grimwood, J., Jenkins, J., Shu, S., Song, Q., Chavarro, C., Geffroy, V., Moghaddam, S.M., Dongying, G., Abernathy, B., Barry, K., Blair, M., Brick, M.A., Chovatia, M., Gepts, P., Goodstein, D.M., Gonzales, M., Hellsten, U., Hyten, D.L., Gaofeng, J., Kelly, J., Kudrna, D., Lee, R., Manon, R.M., Miklas, P.N., Osorno, J.M., Rodrigues, J., Thareau, V., Urrea, C.A., Wang, M., Yu, Y., Zhang, M., Wing, R.A., Cregan, P.B., Rokhsar, D.S., Jackson, S.A. 2014. A reference genome for common bean and genome wide analysis of dual domestications. Nature Genetics. 46: 707-713. DOI: 10.1038/ng.3008.

Interpretive Summary: The whole genome sequence, with 27,000 annotated protein/gene sequences, provides a major genomic tool for interpreting genetic diversity, modeling genes, and dissecting complex traits and processes in common bean. The reference genome herein was used to study common bean domestication and to identify candidate genes underlying seed size QTL. This annotated sequence completes the genomics tool box and provides a reference genome which will impact all subsequent genomic-related studies on common bean.

Technical Abstract: Common bean (Phaseolus vulgaris) is the single most important grain legume for human consumption and, due to its ability to fix atmospheric nitrogen via symbioses with soil-borne microorganisms, has a valuable place in sustainable agriculture. We assembled 473 Mb of the common bean genome and genetically anchored 98% of the sequence in 11 chromosome-scale pseudomolecules. We compared the common bean genome against its most economically important relative, soybean, to examine the changes in soybean after its recent whole genome duplication. Using resequencing of 60 wild individuals and 100 landraces from the two, genetically differentiated Mesoamerican and Andean gene pools, we confirmed that common bean underwent two independent domestications, starting from genetic pools that had diverged prior to human colonization. We used sequence diversity and differentiation estimates to identify a subset of genes linked with an increase in seed associated pathways and seed size and combined these results with QTL data from a multi-site association mapping trial of modern Mesomerican cultivars to identify additional genes that likely contribute to the large seed size of modern, cultivated common bean. Finally, we identified a set of genes impacted by domestication as further targets for genomics-enabled crop improvement.

Last Modified: 7/2/2015
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