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

Lindsey J Leach,Carly Brown,Aziz Mithani,Nicholas P Harberd,Caifu Jiang,Eric J Belfield

doi:10.1186/1471-2164-15-276

Lindsey J Leach, Carly Brown + Show 4 more

Open Access

https://doi.org/10.1186/1471-2164-15-276

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Abstract

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.

Highlights

Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets
The nullitetras have historically been used for determining presence of wheat genes on specific homoeologous chromosomes [59,60,61], and we reasoned that, in combination with generation sequencing, they could be used to develop a systematic understanding of the relative contributions of individual homoeoloci to overall wheat gene expression
Homoeolocus-specific sequence analysis shows at least 45% of wheat genes are expressed from all three homoeoloci We developed a novel strategy for the direct detection of wheat sequence variants and their assignment to homoeologous chromosomes using nullitetra analysis

Summary

Introduction

Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Between 3080% of species are currently polyploids [4], while the rest exist as paleopolyploids [5,6], having undergone a gradual process of “diploidization,” or reversion to a diploid state over evolutionary time. This process involves extensive genomic rearrangements, including the physical loss of a large fraction of duplicate regions, and the accumulation of mutations that distinguish the sequences of the duplicate ‘homoeologous’ copies and contribute to their functional divergence [7,8,9]. Allopolyploid plants often undergo major including Arabidopsis [18], maize [19], Brassica [20] and soybean [21,22]

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