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ARS Home » Pacific West Area » Pullman, Washington » Grain Legume Genetics Physiology Research » Research » Publications at this Location » Publication #297686

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 - Phil
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: 5/13/2014
Publication Date: 6/8/2014
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.