Leach Lindsey J, Belfield Eric J, Jiang Caifu, Brown Carly, Mithani Aziz, Harberd Nicholas P
Department of Plant Sciences, University of Oxford, Oxford, UK.
BMC Genomics. 2014 Apr 11;15:276. doi: 10.1186/1471-2164-15-276.
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.
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.
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.
普通小麦（Triticum aestivum）具有庞大、复杂的六倍体基因组，由A、B和D三组同源染色体组成。因此，每个小麦基因可能以A、B和D三个同源基因座的形式存在，每个同源基因座对小麦表型的贡献可能不同。我们描述了一种新方法，将小麦细胞遗传学资源（染色体替代“缺体-四体”系）与基因转录本的下一代深度测序（RNA测序）相结合，以直接准确地鉴定同源基因特异性单核苷酸变异，并量化各个同源基因座对基因表达的相对贡献。
基于涵盖约5%-10%小麦基因总量的样本，我们发现至少45%的小麦基因在所有三个不同的同源基因座上都有表达。这些基因中的大多数表现出明显的偏向性表达模式，其中表达主要由单个同源基因座主导。其余约55%的小麦基因仅从一个或两个同源基因座表达，这是广泛的转录沉默和同源基因座丢失共同作用的结果。
我们得出结论，通过多种机制使单个同源基因座成为基因转录本的主要来源，小麦正趋向于功能二倍体化。这一发现对小麦育种以及我们对小麦进化的理解具有深远影响。
