Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus

Summary Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two event...

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Published inPlant biotechnology journal Vol. 16; no. 7; pp. 1265 - 1274
Main Authors Hurgobin, Bhavna, Golicz, Agnieszka A., Bayer, Philipp E., Chan, Chon‐Kit Kenneth, Tirnaz, Soodeh, Dolatabadian, Aria, Schiessl, Sarah V., Samans, Birgit, Montenegro, Juan D., Parkin, Isobel A. P., Pires, J. Chris, Chalhoub, Boulos, King, Graham J., Snowdon, Rod, Batley, Jacqueline, Edwards, David
Format Journal Article
LanguageEnglish
Published England John Wiley & Sons, Inc 01.07.2018
Wiley
John Wiley and Sons Inc
Subjects
agronomic traits
Agronomy
amphidiploidy
Brassica
Brassica napus
Brassica napus - genetics
canola
Diploidy
Disease resistance
Exchanging
Flow resistance
Flowering
flowering date
Gene Conversion - genetics
Gene Deletion
Gene Duplication
Genes
Genes, Plant - genetics
Genetic diversity
genetic variation
Genetic Variation - genetics
genome structure
Genome, Plant - genetics
glucosinolates
Life Sciences
Lipid metabolism
Metabolism
pangenome
phenotype
Phenotypes
Polyploidy
Quantitative Trait, Heritable
Rape plants
recombination
Vegetal Biology
Brassica napus
pangenome
recombination
genome structure
canola
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Abstract Summary Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HEs and PAVs in B. napus at the pangenome level.
AbstractList Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HEs and PAVs in B. napus at the pangenome level.Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HEs and PAVs in B. napus at the pangenome level.
Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HEs and PAVs in B. napus at the pangenome level.
Summary Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HEs and PAVs in B. napus at the pangenome level.
Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HEs and PAVs in B. napus at the pangenome level.
Homoeologous exchanges ( HE s) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation ( PAV ) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HE s and PAV s in B. napus at the pangenome level.
Homoeologous exchanges ( HE s) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation ( PAV ) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HE s and PAV s in B. napus at the pangenome level.
Author Dolatabadian, Aria
Schiessl, Sarah V.
Pires, J. Chris
Parkin, Isobel A. P.
Chalhoub, Boulos
Golicz, Agnieszka A.
Edwards, David
Snowdon, Rod
Tirnaz, Soodeh
Chan, Chon‐Kit Kenneth
Bayer, Philipp E.
Hurgobin, Bhavna
Montenegro, Juan D.
King, Graham J.
Batley, Jacqueline
Samans, Birgit
AuthorAffiliation 2 School of Agriculture and Food Sciences University of Queensland St. Lucia QLD Australia
3 Plant Molecular Biology and Biotechnology Laboratory Faculty of Veterinary and Agricultural Sciences University of Melbourne Melbourne VIC Australia
7 Institute of System and Synthetic Biology, Organization and Evolution of Complex Genomes Institut National de la Recherche agronomique, Genopole Centre National de la Recherche Scientifique Université d'Evry Val d'Essonne Université Paris‐Saclay Evry France
6 Division of Biological Sciences University of Missouri Columbia MO USA
1 School of Biological Sciences and Institute of Agriculture The University of Western Australia Crawley WA Australia
4 Department of Plant Breeding IFZ Research Centre for Biosystems, Land Use and Nutrition Justus Liebig University Giessen Germany
5 Agriculture and Agri‐Food Canada Saskatoon SK Canada
8 Southern Cross Plant Science Southern Cross University Lismore NSW Australia
AuthorAffiliation_xml – name: 3 Plant Molecular Biology and Biotechnology Laboratory Faculty of Veterinary and Agricultural Sciences University of Melbourne Melbourne VIC Australia
– name: 7 Institute of System and Synthetic Biology, Organization and Evolution of Complex Genomes Institut National de la Recherche agronomique, Genopole Centre National de la Recherche Scientifique Université d'Evry Val d'Essonne Université Paris‐Saclay Evry France
– name: 8 Southern Cross Plant Science Southern Cross University Lismore NSW Australia
– name: 2 School of Agriculture and Food Sciences University of Queensland St. Lucia QLD Australia
– name: 4 Department of Plant Breeding IFZ Research Centre for Biosystems, Land Use and Nutrition Justus Liebig University Giessen Germany
– name: 6 Division of Biological Sciences University of Missouri Columbia MO USA
– name: 1 School of Biological Sciences and Institute of Agriculture The University of Western Australia Crawley WA Australia
– name: 5 Agriculture and Agri‐Food Canada Saskatoon SK Canada
Author_xml – sequence: 1
  givenname: Bhavna
  surname: Hurgobin
  fullname: Hurgobin, Bhavna
  organization: University of Queensland
– sequence: 2
  givenname: Agnieszka A.
  orcidid: 0000-0002-9711-4826
  surname: Golicz
  fullname: Golicz, Agnieszka A.
  organization: University of Melbourne
– sequence: 3
  givenname: Philipp E.
  orcidid: 0000-0001-8530-3067
  surname: Bayer
  fullname: Bayer, Philipp E.
  organization: The University of Western Australia
– sequence: 4
  givenname: Chon‐Kit Kenneth
  orcidid: 0000-0003-0413-6397
  surname: Chan
  fullname: Chan, Chon‐Kit Kenneth
  organization: The University of Western Australia
– sequence: 5
  givenname: Soodeh
  orcidid: 0000-0002-6100-1790
  surname: Tirnaz
  fullname: Tirnaz, Soodeh
  organization: The University of Western Australia
– sequence: 6
  givenname: Aria
  orcidid: 0000-0002-2158-4485
  surname: Dolatabadian
  fullname: Dolatabadian, Aria
  organization: The University of Western Australia
– sequence: 7
  givenname: Sarah V.
  orcidid: 0000-0003-4372-858X
  surname: Schiessl
  fullname: Schiessl, Sarah V.
  organization: Justus Liebig University
– sequence: 8
  givenname: Birgit
  surname: Samans
  fullname: Samans, Birgit
  organization: Justus Liebig University
– sequence: 9
  givenname: Juan D.
  surname: Montenegro
  fullname: Montenegro, Juan D.
  organization: University of Queensland
– sequence: 10
  givenname: Isobel A. P.
  surname: Parkin
  fullname: Parkin, Isobel A. P.
  organization: Agriculture and Agri‐Food Canada
– sequence: 11
  givenname: J. Chris
  surname: Pires
  fullname: Pires, J. Chris
  organization: University of Missouri
– sequence: 12
  givenname: Boulos
  surname: Chalhoub
  fullname: Chalhoub, Boulos
  organization: Université Paris‐Saclay
– sequence: 13
  givenname: Graham J.
  surname: King
  fullname: King, Graham J.
  organization: Southern Cross University
– sequence: 14
  givenname: Rod
  surname: Snowdon
  fullname: Snowdon, Rod
  organization: Justus Liebig University
– sequence: 15
  givenname: Jacqueline
  orcidid: 0000-0002-5391-5824
  surname: Batley
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  organization: The University of Western Australia
– sequence: 16
  givenname: David
  orcidid: 0000-0001-7599-6760
  surname: Edwards
  fullname: Edwards, David
  email: dave.edwards@uwa.edu.au
  organization: The University of Western Australia
BackLink https://www.ncbi.nlm.nih.gov/pubmed/29205771$$D View this record in MEDLINE/PubMed
https://hal.inrae.fr/hal-02628974$$DView record in HAL
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Copyright 2017 The Authors. published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
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Issue 7
Keywords Brassica napus
pangenome
recombination
genome structure
canola
Language English
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Snippet Summary Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence...
Homoeologous exchanges ( HE s) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence...
Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence...
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StartPage 1265
SubjectTerms agronomic traits
Agronomy
amphidiploidy
Brassica
Brassica napus
Brassica napus - genetics
canola
Diploidy
Disease resistance
Exchanging
Flow resistance
Flowering
flowering date
Gene Conversion - genetics
Gene Deletion
Gene Duplication
Genes
Genes, Plant - genetics
Genetic diversity
genetic variation
Genetic Variation - genetics
genome structure
Genome, Plant - genetics
glucosinolates
Life Sciences
Lipid metabolism
Metabolism
pangenome
phenotype
Phenotypes
Polyploidy
Quantitative Trait, Heritable
Rape plants
recombination
Vegetal Biology
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Title Homoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus
URI https://onlinelibrary.wiley.com/doi/abs/10.1111%2Fpbi.12867
https://www.ncbi.nlm.nih.gov/pubmed/29205771
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Volume 16
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