High‐density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool

In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to br...

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Published inPlant biotechnology journal Vol. 14; no. 5; pp. 1195 - 1206
Main Authors Winfield, Mark O, Allen, Alexandra M, Burridge, Amanda J, Barker, Gary L. A, Benbow, Harriet R, Wilkinson, Paul A, Coghill, Jane, Waterfall, Christy, Davassi, Alessandro, Scopes, Geoff, Pirani, Ali, Webster, Teresa, Brew, Fiona, Bloor, Claire, King, Julie, West, Claire, Griffiths, Simon, King, Ian, Bentley, Alison R, Edwards, Keith J
Format Journal Article
LanguageEnglish
Published England Blackwell Pub 01.05.2016
John Wiley & Sons, Inc
John Wiley and Sons Inc
Subjects
agronomic traits
Agronomy
Arrays
Bread
Breeding
breeding lines
Chromosomes
Consortia
Density
diploidy
Gene Pool
Genes
genetic background
Genetic diversity
Genetic Markers
Genetic variability
Genetic Variation
Genome, Plant - genetics
Genomes
Genotype
Genotype & phenotype
Genotyping
genotyping array
Genotyping Techniques
Goat grass
hexaploidy
Hybridization
introgression
Markers
next‐generation sequencing
Nucleotides
Oligonucleotide Array Sequence Analysis - methods
Polymorphism, Single Nucleotide
Polyploidy
secondary and tertiary gene pools
Single-nucleotide polymorphism
tetraploidy
Triticum - genetics
Triticum aestivum
Websites
Wheat
wheat progenitors
United Kingdom > UK
secondary and tertiary gene pools
wheat
next-generation sequencing
single nucleotide polymorphism
genotyping array
wheat progenitors
Online AccessGet full text

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Abstract In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra‐high‐density Axiom® genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.
AbstractList In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra-high-density Axiom(®) genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.
In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra‐high‐density Axiom ® genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.
In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra-high-density Axiom[sup.®] genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.
In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra‐high‐density Axiom® genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.
Summary In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra‐high‐density Axiom® genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.
In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra-high-density Axiom super( registered ) genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.
Audience Academic
Author Benbow, Harriet R
Allen, Alexandra M
Winfield, Mark O
Bloor, Claire
Waterfall, Christy
King, Julie
Coghill, Jane
Brew, Fiona
Edwards, Keith J
Burridge, Amanda J
West, Claire
Wilkinson, Paul A
Bentley, Alison R
Davassi, Alessandro
Griffiths, Simon
Webster, Teresa
Scopes, Geoff
Barker, Gary L. A
Pirani, Ali
King, Ian
AuthorAffiliation 1 Life Sciences University of Bristol Bristol UK
5 The John Bingham Laboratory NIAB Cambridge UK
4 John Innes Centre Norwich Research Park Norwich Norfolk UK
2 Affymetrix UK Ltd High Wycombe UK
3 School of Biosciences Sutton Bonington Leicestershire UK
AuthorAffiliation_xml – name: 1 Life Sciences University of Bristol Bristol UK
– name: 3 School of Biosciences Sutton Bonington Leicestershire UK
– name: 5 The John Bingham Laboratory NIAB Cambridge UK
– name: 4 John Innes Centre Norwich Research Park Norwich Norfolk UK
– name: 2 Affymetrix UK Ltd High Wycombe UK
Author_xml – sequence: 1
  fullname: Winfield, Mark O
– sequence: 2
  fullname: Allen, Alexandra M
– sequence: 3
  fullname: Burridge, Amanda J
– sequence: 4
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– sequence: 5
  fullname: Benbow, Harriet R
– sequence: 6
  fullname: Wilkinson, Paul A
– sequence: 7
  fullname: Coghill, Jane
– sequence: 8
  fullname: Waterfall, Christy
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  fullname: Davassi, Alessandro
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  fullname: Pirani, Ali
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  fullname: Edwards, Keith J
BackLink https://www.ncbi.nlm.nih.gov/pubmed/26466852$$D View this record in MEDLINE/PubMed
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Copyright 2015 The Authors. published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
2015 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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2016. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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– notice: 2016. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
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Issue 5
Keywords secondary and tertiary gene pools
wheat
next-generation sequencing
single nucleotide polymorphism
genotyping array
wheat progenitors
Language English
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2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.
This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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Snippet In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread...
Summary In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to...
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StartPage 1195
SubjectTerms agronomic traits
Agronomy
Arrays
Bread
Breeding
breeding lines
Chromosomes
Consortia
Density
diploidy
Gene Pool
Genes
genetic background
Genetic diversity
Genetic Markers
Genetic variability
Genetic Variation
Genome, Plant - genetics
Genomes
Genotype
Genotype & phenotype
Genotyping
genotyping array
Genotyping Techniques
Goat grass
hexaploidy
Hybridization
introgression
Markers
next‐generation sequencing
Nucleotides
Oligonucleotide Array Sequence Analysis - methods
Polymorphism, Single Nucleotide
Polyploidy
secondary and tertiary gene pools
Single-nucleotide polymorphism
tetraploidy
Triticum - genetics
Triticum aestivum
Websites
Wheat
wheat progenitors
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Title High‐density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool
URI https://onlinelibrary.wiley.com/doi/abs/10.1111%2Fpbi.12485
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Volume 14
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