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

BMC Genomics

Research Article

Caifu Jiang¹  Nicholas P Harberd¹  Carly Brown¹  Eric J Belfield¹  Lindsey J Leach²  Aziz Mithani³ 

[1] Department of Plant Sciences, University of Oxford, Oxford, UK;Department of Plant Sciences, University of Oxford, Oxford, UK;School of Biosciences, University of Birmingham, Birmingham, UK;Department of Plant Sciences, University of Oxford, Oxford, UK;Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan;

关键词: Wheat;    Wheat transcriptome;    mRNA-Seq;    Diploidization;    Homoeologues;    Polyploidy;   

DOI  :  10.1186/1471-2164-15-276

 received in 2013-11-07, accepted in 2014-04-02,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundBread 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.ResultsWe 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.ConclusionsWe 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.

【 授权许可】

Unknown   
© Leach et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.