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Open Access Research article

Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat

Lindsey J Leach12, Eric J Belfield1, Caifu Jiang1, Carly Brown1, Aziz Mithani13 and Nicholas P Harberd1*

Author Affiliations

1 Department of Plant Sciences, University of Oxford, Oxford, UK

2 School of Biosciences, University of Birmingham, Birmingham, UK

3 Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan

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BMC Genomics 2014, 15:276  doi:10.1186/1471-2164-15-276

Published: 11 April 2014

Abstract

Background

Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoloci, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution ‘nullisomic-tetrasomic’ lines) with next generation deep sequencing of gene transcripts (RNA-Seq), to directly and accurately identify homoeologue-specific single nucleotide variants and quantify the relative contribution of individual homoeoloci to gene expression.

Results

We discover, based on a sample comprising ~5-10% of the total wheat gene content, that at least 45% of wheat genes are expressed from all three distinct homoeoloci. Most of these genes show strikingly biased expression patterns in which expression is dominated by a single homoeolocus. The remaining ~55% of wheat genes are expressed from either one or two homoeoloci only, through a combination of extensive transcriptional silencing and homoeolocus loss.

Conclusions

We conclude that wheat is tending towards functional diploidy, through a variety of mechanisms causing single homoeoloci to become the predominant source of gene transcripts. This discovery has profound consequences for wheat breeding and our understanding of wheat evolution.

Keywords:
Wheat; Wheat transcriptome; mRNA-Seq; Diploidization; Homoeologues; Polyploidy