Department of Life Sciences, Ben-Gurion University, 84105, Beer-Sheva, Israel.
BMC Plant Biol. 2017 Oct 27;17(1):175. doi: 10.1186/s12870-017-1134-z.
Natural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make up a significant part of the genetic and epigenetic variation between individuals and populations because they comprise over 80% of the wild emmer wheat genome. In this study, we performed detailed analyses to assess the dynamics of transposable elements in 50 accessions of wild emmer wheat collected from 5 geographically isolated sites. The analyses included: the copy number variation of TEs among accessions in the five populations, population-unique insertional patterns, and the impact of population-unique/specific TE insertions on structure and expression of genes.
We assessed the copy numbers of 12 TE families using real-time quantitative PCR, and found significant copy number variation (CNV) in the 50 wild emmer wheat accessions, in a population-specific manner. In some cases, the CNV difference reached up to 6-fold. However, the CNV was TE-specific, namely some TE families showed higher copy numbers in one or more populations, and other TE families showed lower copy numbers in the same population(s). Furthermore, we assessed the insertional patterns of 6 TE families using transposon display (TD), and observed significant population-specific insertional patterns. The polymorphism levels of TE-insertional patterns reached 92% among all wild emmer wheat accessions, in some cases. In addition, we observed population-specific/unique TE insertions, some of which were located within or close to protein-coding genes, creating allelic variations in a population-specific manner. We also showed that those genes are differentially expressed in wild emmer wheat.
For the first time, this study shows that TEs proliferate in wild emmer wheat in a population-specific manner, creating new alleles of genes, which contribute to the divergent evolution of homeologous genes from the A and B subgenomes.
先前的研究表明，四倍体野生二粒小麦（基因组 AABB）的自然种群表现出具有生态地理结构的遗传和表观遗传多样性。转座元件（TEs）可能构成个体和种群之间遗传和表观遗传变异的重要组成部分，因为它们占野生二粒小麦基因组的 80%以上。在这项研究中，我们对来自 5 个地理隔离地点的 50 个野生二粒小麦品系进行了详细分析，以评估转座元件的动态。分析包括：五个群体中品系之间 TEs 的拷贝数变异、群体特有的插入模式以及群体特有/特有的 TE 插入对基因结构和表达的影响。
我们使用实时定量 PCR 评估了 12 个 TE 家族的拷贝数，发现 50 个野生二粒小麦品系的拷贝数存在显著的群体特异性变化。在某些情况下，CNV 差异高达 6 倍。然而，CNV 是 TE 特异性的，即一些 TE 家族在一个或多个群体中显示出较高的拷贝数，而其他 TE 家族在同一群体中显示出较低的拷贝数。此外，我们使用转座子显示（TD）评估了 6 个 TE 家族的插入模式，观察到显著的群体特异性插入模式。在所有野生二粒小麦品系中，TE 插入模式的多态性水平达到 92%，在某些情况下。此外，我们观察到群体特异性/独特的 TE 插入，其中一些位于蛋白质编码基因内或附近，以群体特异性的方式产生等位基因变异。我们还表明，这些基因在野生二粒小麦中差异表达。
本研究首次表明，TEs 以群体特异性的方式在野生二粒小麦中增殖，产生基因的新等位基因，这有助于 A 和 B 亚基因组同源基因的分化进化。
