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, David A 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 journalArticle

456 Citations (Scopus)

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 languageEnglish (US)
Pages (from-to)707-713
Number of pages7
JournalNature Genetics
Volume46
Issue number7
DOIs
StatePublished - 2014

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Genome
Soybeans
Gene Pool
Chromosomes, Human, Pair 11
Polyploidy
Phaseolus
Cotyledon
Quantitative Trait Loci
Genomics
Agriculture
Fabaceae
Genes
Nitrogen
Domestication

ASJC Scopus subject areas

  • Genetics

Cite this

Schmutz, J., McClean, P. E., Mamidi, S., Wu, G. A., Cannon, S. B., Grimwood, J., ... 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

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

In: Nature Genetics, Vol. 46, No. 7, 2014, p. 707-713.

Research output: Contribution to journalArticle

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, DA, 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
Schmutz J, McClean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J et al. A reference genome for common bean and genome-wide analysis of dual domestications. Nature Genetics. 2014;46(7):707-713. https://doi.org/10.1038/ng.3008
Schmutz, Jeremy ; McClean, Phillip E. ; Mamidi, Sujan ; Wu, G. Albert ; Cannon, Steven B. ; Grimwood, Jane ; Jenkins, Jerry ; Shu, Shengqiang ; Song, Qijian ; Chavarro, Carolina ; Torres-Torres, Mirayda ; Geffroy, Valerie ; Moghaddam, Samira Mafi ; Gao, Dongying ; Abernathy, Brian ; Barry, Kerrie ; Blair, Matthew ; Brick, Mark A. ; Chovatia, Mansi ; Gepts, Paul ; Goodstein, David M. ; Gonzales, Michael ; Hellsten, Uffe ; Hyten, David L. ; Jia, Gaofeng ; Kelly, James D. ; Kudrna, David A ; Lee, Rian ; Richard, Manon M S ; Miklas, Phillip N. ; Osorno, Juan M. ; Rodrigues, Josiane ; Thareau, Vincent ; Urrea, Carlos A. ; Wang, Mei ; Yu, Yeisoo ; Zhang, Ming ; Wing, Rod A ; Cregan, Perry B. ; Rokhsar, Daniel S. ; Jackson, Scott A. / A reference genome for common bean and genome-wide analysis of dual domestications. In: Nature Genetics. 2014 ; Vol. 46, No. 7. pp. 707-713.
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