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Homoeologous exchanges cause extensive dosage‐dependent gene expression changes in an allopolyploid crop
Author(s) -
Lloyd Andrew,
Blary Aurélien,
Charif Delphine,
Charpentier Catherine,
Tran Joseph,
Balzergue Sandrine,
Delannoy Etienne,
Rigaill Guillem,
Jenczewski Eric
Publication year - 2018
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.14836
Subject(s) - biology , gene dosage , gene expression , gene , genetics , crop , expression (computer science) , evolutionary biology , botany , agronomy , computer science , programming language
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 HE s. 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.