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ARS Home » Pacific West Area » Pullman, Washington » Grain Legume Genetics Physiology Research » Research » Publications at this Location » Publication #297686
Title: A reference genome for common bean and genome wide analysis of dual domestications

Author
item SHMUTZ, JEREMY - Department Of Energy Joint Genome
item MCCLEAN, PHILLIP - North Dakota State University
item MAMIDI, SUJAN - North Dakota State University
item WU, ALBERT - Department Of Energy Joint Genome
item Cannon, Steven
item GRIMWOOD, JANE - Hudsonalpha Institute For Biotechnology
item JENKINS, JERRY - Hudsonalpha Institute For Biotechnology
item SHU, SHENQIANG - Department Of Energy Joint Genome
item Song, Qijian
item CHAVARRO, CAROLINA - University Of Georgia
item GEFFROY, VALERIE - University Of Paris
item MOGHADDAM, SAMIRA - North Dakota State University
item DONGYING, GAO - University Of Georgia
item ABERNATHY, BRIAN - University Of Georgia
item BARRY, KERRIE - Department Of Energy Joint Genome
item BLAIR, MATTHEW - University Of Georgia
item BRICK, MARK - Colorado State University
item CHOVATIA, MANSI - Department Of Energy Joint Genome
item GEPTS, PAUL - University Of California
item GOODSTEIN, DAVID - Department Of Energy Joint Genome
item GONZALES, MICHAEL - University Of Georgia
item HELLSTEN, UFFE - Department Of Energy Joint Genome
item Hyten, David
item GAOFENG, JIA - Former ARS Employee
item KELLY, JIM - Michigan State University
item KUDRNA, DAVE - University Of Arizona
item LEE, RIAN - North Dakota State University
item MANON, RICHARD - University Of Paris
item Miklas, Phillip - Phil
item OSORNO, JUAN - North Dakota State University
item RODRIGUES, JOSIANE - Former ARS Employee
item THAREAU, VINCENT - University Of Paris
item URREA, CARLOS - University Of Nebraska
item WANG, MEI - Department Of Energy Joint Genome
item YU, YEISOO - University Of Arizona
item ZHANG, MING - Department Of Energy Joint Genome
item WING, ROD - University Of Arizona
item Cregan, Perry
item ROKHSAR, DANIEL - Department Of Energy Joint Genome
item JACKSON, SCOTT - University Of Georgia

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.