The pangenome of an agronomically important crop plant Brassica oleracea

Agnieszka A. Golicz; Philipp E. Bayer; Guy C. Barker; Patrick P. Edger; Hye Ran Kim; Paula A. Martinez; Chon Kit Kenneth Chan; Anita Severn-Ellis; W. Richard McCombie; Isobel A P Parkin; Andrew H. Paterson; J. Chris Pires; Andrew G. Sharpe; Haibao Tang; Graham R. Teakle; Christopher D. Town; Jacqueline Batley; David Edwards

doi:10.1038/ncomms13390

The pangenome of an agronomically important crop plant Brassica oleracea

Agnieszka A. Golicz
, Philipp E. Bayer
, Guy C. Barker
, Patrick P. Edger
, Hye Ran Kim
, Paula A. Martinez
, Chon Kit Kenneth Chan
, Anita Severn-Ellis
, W. Richard McCombie
, Isobel A P Parkin
, Andrew H. Paterson
, J. Chris Pires
, Andrew G. Sharpe
, Haibao Tang
, Graham R. Teakle
, Christopher D. Town
, Jacqueline Batley
, David Edwards

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

445 Citations (Scopus)

Abstract

There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.

Original language	English
Article number	13390
Journal	Nature Communications
Volume	7
DOIs	https://doi.org/10.1038/ncomms13390
Publication status	Published - 11 Nov 2016

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 2 Zero Hunger

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10.1038/ncomms13390Licence: CC BY

Cite this

Golicz, A. A., Bayer, P. E., Barker, G. C., Edger, P. P., Kim, H. R., Martinez, P. A., Chan, C. K. K., Severn-Ellis, A., McCombie, W. R., Parkin, I. A. P., Paterson, A. H., Pires, J. C., Sharpe, A. G., Tang, H., Teakle, G. R., Town, C. D., Batley, J., & Edwards, D. (2016). The pangenome of an agronomically important crop plant Brassica oleracea. Nature Communications, 7, Article 13390. https://doi.org/10.1038/ncomms13390

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title = "The pangenome of an agronomically important crop plant Brassica oleracea",

abstract = "There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20\% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.",

author = "Golicz, \{Agnieszka A.\} and Bayer, \{Philipp E.\} and Barker, \{Guy C.\} and Edger, \{Patrick P.\} and Kim, \{Hye Ran\} and Martinez, \{Paula A.\} and Chan, \{Chon Kit Kenneth\} and Anita Severn-Ellis and McCombie, \{W. Richard\} and Parkin, \{Isobel A P\} and Paterson, \{Andrew H.\} and Pires, \{J. Chris\} and Sharpe, \{Andrew G.\} and Haibao Tang and Teakle, \{Graham R.\} and Town, \{Christopher D.\} and Jacqueline Batley and David Edwards",

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Golicz, AA, Bayer, PE, Barker, GC, Edger, PP, Kim, HR, Martinez, PA, Chan, CKK, Severn-Ellis, A, McCombie, WR, Parkin, IAP, Paterson, AH, Pires, JC, Sharpe, AG, Tang, H, Teakle, GR, Town, CD, Batley, J & Edwards, D 2016, 'The pangenome of an agronomically important crop plant Brassica oleracea', Nature Communications, vol. 7, 13390. https://doi.org/10.1038/ncomms13390

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AU - Golicz, Agnieszka A.

AU - Bayer, Philipp E.

AU - Barker, Guy C.

AU - Edger, Patrick P.

AU - Kim, Hye Ran

AU - Martinez, Paula A.

AU - Chan, Chon Kit Kenneth

AU - Severn-Ellis, Anita

AU - McCombie, W. Richard

AU - Parkin, Isobel A P

AU - Paterson, Andrew H.

AU - Pires, J. Chris

AU - Sharpe, Andrew G.

AU - Tang, Haibao

AU - Teakle, Graham R.

AU - Town, Christopher D.

AU - Batley, Jacqueline

AU - Edwards, David

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AB - There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.

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VL - 7

JO - Nature Communications

JF - Nature Communications

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ER -

The pangenome of an agronomically important crop plant Brassica oleracea

Abstract

UN SDGs

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The More the Merrier? Investigating copy number variation in Brassicas

Establishing Novel Breeding Methods for Canola Improvement

Defining the Brassica Pan-genome and Establishing Methods for Gene Conversion Based Crop Improvement

Cite this

The pangenome of an agronomically important crop plant Brassica oleracea

Abstract

UN SDGs

Access to Document

Other files and links

Fingerprint

Projects

The More the Merrier? Investigating copy number variation in Brassicas

Establishing Novel Breeding Methods for Canola Improvement

Defining the Brassica Pan-genome and Establishing Methods for Gene Conversion Based Crop Improvement

Cite this