Development of the GlutEnSeq capture system for sequencing gluten gene families in hexaploid bread wheat with deletions or mutations induced by γ-irradiation or CRISPR/Cas9

Aurélie Jouanin, Theo Borm, Lesley A. Boyd, James Cockram, Fiona Leigh, Bruno A.C.M. Santos, Richard G.F. Visser, Marinus J.M. Smulders

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

We developed an in-solution gluten exome capture system called GlutEnSeq (Gluten gene Enrichment and Sequencing), covering the sequence variation of thousands of prolamin genes from various Triticeae species and cultivars. We assessed the efficacy of this capture system in hexaploid wheat (Triticum aestivum L.) using Illumina sequencing. On-target regions were determined based on the Chinese Spring (CS) reference genome sequence. Gluten gene sequences were generally enriched around 10,000-fold. The loss of gluten genes in CS deletion line 1BS-19/6DS-4 was detected as absence of gluten gene coverage on chromosomes 1B and Un (containing the Unmapped α-gliadin genes of chromosome 6D). Two γ-irradiated lines of cultivar Paragon, shown to be affected in their gliadin protein profile, were found to contain homozygous deletions for the α-gliadins on 6A and the γ-gliadins on 1B. Four Fielder CRISPR/Cas9 gliadin gene-edited lines revealed homozygous deletions of the γ-gliadins on 1B and heterozygous deletions for the α-gliadins on 6A. We also detected a decrease of gluten gene coverage within some gluten genes. The bioinformatics pipeline developed here will be further optimised to enable characterisation of small indels within individual gluten genes, in order to fully analyse CRISPR/Cas9 mutant lines for their decrease in immunogenicity for Coeliac patients.

LanguageEnglish
Pages157-166
Number of pages10
JournalJournal of Cereal Science
Volume88
DOIs
Publication statusPublished - 1 Jul 2019

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Clustered Regularly Interspaced Short Palindromic Repeats
Glutens
Sequence Deletion
Bread
hexaploidy
Gliadin
gluten
mutagenesis
Triticum
gamma radiation
gliadin
Genes
Irradiation
wheat
genes
Chromosomes
Prolamins
Exome
chromosomes
prolamins

Keywords

  • Breeding
  • Coeliac
  • Disease
  • Editing
  • Gene
  • Gliadin
  • Mutation

Cite this

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title = "Development of the GlutEnSeq capture system for sequencing gluten gene families in hexaploid bread wheat with deletions or mutations induced by γ-irradiation or CRISPR/Cas9",
abstract = "We developed an in-solution gluten exome capture system called GlutEnSeq (Gluten gene Enrichment and Sequencing), covering the sequence variation of thousands of prolamin genes from various Triticeae species and cultivars. We assessed the efficacy of this capture system in hexaploid wheat (Triticum aestivum L.) using Illumina sequencing. On-target regions were determined based on the Chinese Spring (CS) reference genome sequence. Gluten gene sequences were generally enriched around 10,000-fold. The loss of gluten genes in CS deletion line 1BS-19/6DS-4 was detected as absence of gluten gene coverage on chromosomes 1B and Un (containing the Unmapped α-gliadin genes of chromosome 6D). Two γ-irradiated lines of cultivar Paragon, shown to be affected in their gliadin protein profile, were found to contain homozygous deletions for the α-gliadins on 6A and the γ-gliadins on 1B. Four Fielder CRISPR/Cas9 gliadin gene-edited lines revealed homozygous deletions of the γ-gliadins on 1B and heterozygous deletions for the α-gliadins on 6A. We also detected a decrease of gluten gene coverage within some gluten genes. The bioinformatics pipeline developed here will be further optimised to enable characterisation of small indels within individual gluten genes, in order to fully analyse CRISPR/Cas9 mutant lines for their decrease in immunogenicity for Coeliac patients.",
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author = "Aur{\'e}lie Jouanin and Theo Borm and Boyd, {Lesley A.} and James Cockram and Fiona Leigh and Santos, {Bruno A.C.M.} and Visser, {Richard G.F.} and Smulders, {Marinus J.M.}",
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Development of the GlutEnSeq capture system for sequencing gluten gene families in hexaploid bread wheat with deletions or mutations induced by γ-irradiation or CRISPR/Cas9. / Jouanin, Aurélie; Borm, Theo; Boyd, Lesley A.; Cockram, James; Leigh, Fiona; Santos, Bruno A.C.M.; Visser, Richard G.F.; Smulders, Marinus J.M.

In: Journal of Cereal Science, Vol. 88, 01.07.2019, p. 157-166.

Research output: Contribution to journalArticleAcademicpeer-review

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T1 - Development of the GlutEnSeq capture system for sequencing gluten gene families in hexaploid bread wheat with deletions or mutations induced by γ-irradiation or CRISPR/Cas9

AU - Jouanin, Aurélie

AU - Borm, Theo

AU - Boyd, Lesley A.

AU - Cockram, James

AU - Leigh, Fiona

AU - Santos, Bruno A.C.M.

AU - Visser, Richard G.F.

AU - Smulders, Marinus J.M.

PY - 2019/7/1

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N2 - We developed an in-solution gluten exome capture system called GlutEnSeq (Gluten gene Enrichment and Sequencing), covering the sequence variation of thousands of prolamin genes from various Triticeae species and cultivars. We assessed the efficacy of this capture system in hexaploid wheat (Triticum aestivum L.) using Illumina sequencing. On-target regions were determined based on the Chinese Spring (CS) reference genome sequence. Gluten gene sequences were generally enriched around 10,000-fold. The loss of gluten genes in CS deletion line 1BS-19/6DS-4 was detected as absence of gluten gene coverage on chromosomes 1B and Un (containing the Unmapped α-gliadin genes of chromosome 6D). Two γ-irradiated lines of cultivar Paragon, shown to be affected in their gliadin protein profile, were found to contain homozygous deletions for the α-gliadins on 6A and the γ-gliadins on 1B. Four Fielder CRISPR/Cas9 gliadin gene-edited lines revealed homozygous deletions of the γ-gliadins on 1B and heterozygous deletions for the α-gliadins on 6A. We also detected a decrease of gluten gene coverage within some gluten genes. The bioinformatics pipeline developed here will be further optimised to enable characterisation of small indels within individual gluten genes, in order to fully analyse CRISPR/Cas9 mutant lines for their decrease in immunogenicity for Coeliac patients.

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KW - Breeding

KW - Coeliac

KW - Disease

KW - Editing

KW - Gene

KW - Gliadin

KW - Mutation

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JO - Journal of Cereal Science

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JF - Journal of Cereal Science

SN - 0733-5210

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