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

doi:10.1038/ng.3008

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 GeptsDavid 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

Research output: Contribution to journal › Article › peer-review

930 Scopus citations

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.

Original language	English (US)
Pages (from-to)	707-713
Number of pages	7
Journal	Nature Genetics
Volume	46
Issue number	7
DOIs	https://doi.org/10.1038/ng.3008
State	Published - Jul 2014

ASJC Scopus subject areas

Genetics

Access to Document

10.1038/ng.3008

Cite this

Schmutz, J., McClean, P. E., Mamidi, S., Wu, G. A., Cannon, S. B., Grimwood, J., Jenkins, J., Shu, S., Song, Q., Chavarro, C., Torres-Torres, M., Geffroy, V., Moghaddam, S. M., Gao, D., Abernathy, B., Barry, K., Blair, M., Brick, M. A., Chovatia, M., ... Jackson, S. A. (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics, 46(7), 707-713. https://doi.org/10.1038/ng.3008

Schmutz, J, McClean, PE, Mamidi, S, Wu, GA, Cannon, SB, Grimwood, J, Jenkins, J, Shu, S, Song, Q, Chavarro, C, Torres-Torres, M, Geffroy, V, Moghaddam, SM, Gao, D, Abernathy, B, Barry, K, Blair, M, Brick, MA, Chovatia, M, Gepts, P, Goodstein, DM, Gonzales, M, Hellsten, U, Hyten, DL, Jia, G, Kelly, JD, Kudrna, D, Lee, R, Richard, MMS, Miklas, PN, Osorno, JM, Rodrigues, J, Thareau, V, Urrea, CA, Wang, M, Yu, Y, Zhang, M, Wing, RA, Cregan, PB, Rokhsar, DS & Jackson, SA 2014, 'A reference genome for common bean and genome-wide analysis of dual domestications', Nature Genetics, vol. 46, no. 7, pp. 707-713. https://doi.org/10.1038/ng.3008

@article{c053a6b39c74432dae70a6bc5068193d,

title = "A reference genome for common bean and genome-wide analysis of dual domestications",

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.",

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

note = "Funding Information: The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract DE-AC02-05CH11231. This research was funded by grants from the US Department of Agriculture–National Institute for Food and Agriculture (2006-35300-17266) and the National Science Foundation (DBI 0822258) to S.A.J. and from the US Department of Agriculture–Cooperative State Research, Education and Extension Service (2009-01860 and 2009-01929) to S.A.J. and P.E.M., respectively.",

year = "2014",

month = jul,

doi = "10.1038/ng.3008",

language = "English (US)",

volume = "46",

pages = "707--713",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group",

number = "7",

}

TY - JOUR

T1 - A reference genome for common bean and genome-wide analysis of dual domestications

AU - Schmutz, Jeremy

AU - McClean, Phillip E.

AU - Mamidi, Sujan

AU - Wu, G. Albert

AU - Cannon, Steven B.

AU - Grimwood, Jane

AU - Jenkins, Jerry

AU - Shu, Shengqiang

AU - Song, Qijian

AU - Chavarro, Carolina

AU - Torres-Torres, Mirayda

AU - Geffroy, Valerie

AU - Moghaddam, Samira Mafi

AU - Gao, Dongying

AU - Abernathy, Brian

AU - Barry, Kerrie

AU - Blair, Matthew

AU - Brick, Mark A.

AU - Chovatia, Mansi

AU - Gepts, Paul

AU - Goodstein, David M.

AU - Gonzales, Michael

AU - Hellsten, Uffe

AU - Hyten, David L.

AU - Jia, Gaofeng

AU - Kelly, James D.

AU - Kudrna, Dave

AU - Lee, Rian

AU - Richard, Manon M.S.

AU - Miklas, Phillip N.

AU - Osorno, Juan M.

AU - Rodrigues, Josiane

AU - Thareau, Vincent

AU - Urrea, Carlos A.

AU - Wang, Mei

AU - Yu, Yeisoo

AU - Zhang, Ming

AU - Wing, Rod A.

AU - Cregan, Perry B.

AU - Rokhsar, Daniel S.

AU - Jackson, Scott A.

N1 - Funding Information: The work conducted by the US Department of Energy Joint Genome Institute is supported by the Office of Science of the US Department of Energy under contract DE-AC02-05CH11231. This research was funded by grants from the US Department of Agriculture–National Institute for Food and Agriculture (2006-35300-17266) and the National Science Foundation (DBI 0822258) to S.A.J. and from the US Department of Agriculture–Cooperative State Research, Education and Extension Service (2009-01860 and 2009-01929) to S.A.J. and P.E.M., respectively.

PY - 2014/7

Y1 - 2014/7

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84903517143&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84903517143&partnerID=8YFLogxK

U2 - 10.1038/ng.3008

DO - 10.1038/ng.3008

M3 - Article

C2 - 24908249

AN - SCOPUS:84903517143

SN - 1061-4036

VL - 46

SP - 707

EP - 713

JO - Nature Genetics

JF - Nature Genetics

IS - 7

ER -

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

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this