Harper, Andrea Louise orcid.org/0000-0003-3859-1152, Trick, Martin, He, Zhesi orcid.org/0000-0001-8335-9876 et al. (4 more authors) (2015) Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat. Plant biotechnology journal. ISSN 1467-7644
Abstract
Using a combination of de novo transcriptome assembly, a newly-developed 9495-marker transcriptome SNP genetic linkage map and comparative genomics approaches, we developed an ordered set of non-redundant transcripts for each of the sub-genomes of hexaploid wheat: A (47,160 unigenes), B (59,663 unigenes) and D (40,588 unigenes). We used these as reference sequences against which to map Illumina mRNA-seq reads derived from young leaf tissue. Transcript abundance was quantified for each unigene. Using a 3-way reciprocal BLAST approach, 15,527 triplet sets of homoeologues (one from each genome) were identified. Differential expression (P<0.05) was identified for 5,248 unigenes, with 2906 represented at greater abundance than their two homoeologues and 2342 represented at lower abundance than their two homoeologues. Analysis of gene ontology terms revealed no biases between homoeologues. There was no evidence of genome-wide dominance effects, rather the more highly transcribed individual genes were distributed throughout all three genomes. Transcriptome Display Tile Plot (TDTP), a visualization approach based on CMYK colourspace, was developed and used to assess the genome for regions of skewed homoeologue transcript abundance. Extensive striation was revealed, indicative of many small regions of genome dominance (transcripts of homoeologues from one genome more abundant than the others) and many larger regions of genome repression (transcripts of homoeologues from one genome less abundant than the others).
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © 2015 The Authors. This content is made available by the publisher under a Creative Commons CC BY Licence |
Dates: |
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Institution: | The University of York |
Academic Units: | The University of York > Faculty of Sciences (York) > Biology (York) The University of York > Faculty of Sciences (York) > Biology (York) > Centre for Novel Agricultural Products (CNAP) (York) |
Depositing User: | Pure (York) |
Date Deposited: | 22 Dec 2015 15:56 |
Last Modified: | 21 Jan 2025 17:18 |
Published Version: | https://doi.org/10.1111/pbi.12486 |
Status: | Published |
Refereed: | Yes |
Identification Number: | 10.1111/pbi.12486 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:93070 |
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