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

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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. © 2014 Leach et al.; licensee BioMed Central Ltd.

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Leach, L. J., Belfield, E. J., Jiang, C., Brown, C., Mithani, A., & Harberd, N. P. (2014). Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat. BMC Genomics, 15(1). https://doi.org/10.1186/1471-2164-15-276

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