Homoeologous exchanges cause extensive dosage-dependent gene expression changes in an allopolyploid crop

Structural variation is a major source of genetic diversity and an important substrate for selection. In allopolyploids, homoeologous exchanges (i.e. between the constituent subgenomes) are a very frequent type of structural variant. However, their direct impact on gene content and gene expression h...

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Bibliographic Details
Published in:The New phytologist Vol. 217; no. 1; pp. 367 - 377
Main Authors: Lloyd, Andrew, Blary, Aurélien, Charif, Delphine, Charpentier, Catherine, Tran, Joseph, Balzergue, Sandrine, Delannoy, Etienne, Rigaill, Guillem, Jenczewski, Eric
Format: Journal Article
Language:English
Published: England New Phytologist Trust 01.01.2018
Wiley Subscription Services, Inc
Wiley
Subjects:
allopolyploidy
Brassica
Brassica napus
Brassica napus (Rapeseed)
Brassica napus - genetics
Copy number
copy number variation
data collection
Dosage
Evolution
Gene Dosage
Gene Expression
genes
Genetic diversity
Genetic Variation
Genome, Plant - genetics
Genomes
homoeologous exchanges
Life Sciences
meiotic recombination
Organ Specificity
Polyploidy
Recombination, Genetic
Reproductive Biology
Sequence Analysis, RNA
Sexual reproduction
Tissue
Transcription
transcription (genetics)
meiotic recombination
copy number variation
polyploidy
homoeologous exchanges
Brassica napus (Rapeseed)
gene expression
polyploid
ISSN:0028-646X, 1469-8137, 1469-8137
Online Access:Get full text
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Summary:Structural variation is a major source of genetic diversity and an important substrate for selection. In allopolyploids, homoeologous exchanges (i.e. between the constituent subgenomes) are a very frequent type of structural variant. However, their direct impact on gene content and gene expression had not been determined. Here, we used a tissue-specific mRNA-Seq dataset to measure the consequences of homoeologous exchanges (HE) on gene expression in Brassica napus, a representative allotetraploid crop. We demonstrate that expression changes are proportional to the change in gene copy number triggered by the HEs. Thus, when homoeologous gene pairs have unbalanced transcriptional contributions before the HE, duplication of one copy does not accurately compensate for loss of the other and combined homoeologue expression also changes. These effects are, however, mitigated over time. This study sheds light on the origins, timing and functional consequences of homeologous exchanges in allopolyploids. It demonstrates that the interplay between new structural variation and the resulting impacts on gene expression, influences allopolyploid genome evolution.
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ISSN:0028-646X
1469-8137
1469-8137
DOI:10.1111/nph.14836