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

BMC Genomics

Nicholas P Harberd²  Aziz Mithani¹  Carly Brown²  Caifu Jiang²  Eric J Belfield²  Lindsey J Leach² 

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

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

Others  :  1217490
DOI  :  10.1186/1471-2164-15-276

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

【 摘 要 】

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.

【 授权许可】

   
2014 Leach et al.; licensee BioMed Central Ltd.

【 图 表 】

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