Identification of plant genome segments that change methylation states and its implication for breeding traits

在植物中，表型变异通常是由遗传变化引起的。然而，最近已经表明，表型变异也可能是由异常甲基化状态引起的表观遗传变化引起的。与哺乳动物基因组不同，植物基因组中的DNA甲基化在减数分裂和有丝分裂阶段都被遗传保持。因此，植物基因组片段中改变的甲基化状态可能在后代中传递和维持。本研究包括两部分，以确定存在的基因片段与可变甲基化状态，并了解其机制。首先，我们调查了粳稻、籼稻和野生稻等9个不同水稻品系中甲基化状态发生改变的基因组片段。其次，我们分析了金鱼草转座子Tam 3的去甲基化过程，该转座子的活性受温度的严格控制，并且似乎与其甲基化状态相关。在第一个问题上，我们的结果表明，在非多态性片段中的表观遗传标记的出现似乎与所检测的9个水稻品系中任何两个之间的遗传距离相关。与此相反，在所有的对中，表位标记在包括多态性和非多态性片段在内的片段总数中的比例是恒定的（2-3%）。我们假设水稻基因组间甲基化的表观遗传差异影响了某些表型变异。第二个问题，我们发现金鱼草Tam 3的甲基化水平受Tam 3活性的调控。Tam 3的活性取决于其转座酶结合DNA的能力，这受到生长温度的影响，Tam 3的甲基化/去甲基化是转座的结果，而不是原因。

In plants, phenotypic variations have generally been found to be caused by genetic changes. However, it has recently been shown that phenotypic variations can also be potentially caused by epigenetic changes due to aberrant methylation states. Unlike that in mammalian genomes, DNA methylation in the plant genome was found to be heritably maintained during both meiotic and mitotic phases. Therefore, an altered methylation state in a plant genomic segment might be transmitted and maintained in the progeny. This study consists of two parts to identify presence of genetic segments with variable methylation state and to understand its mechanism. Firstly, we surveyed genomic segments that change methylation state among different nine rice strains including Japonica, Indica and wild rices. Second, we analyzed demethylation process in Antirrhinum transposon Tam3, of which activity is tightly controlled by temperature and appears to be correlated with its methylation state.On the first issue, our results showed that the occurrence of epigenetic (epi)-markers in non-polymorphic fragments appeared to be correlated with the genetic distance between any two of the nine rice strains examined. In contrast, the proportion of epi-markers in the total number of fragments, including polymorphic and non-polymorphic fragments, was constant (2-3%) in all the pairs. We assume that the epigenetic differences in methylation among the rice genomes influence certain phenotypic variations.On the second issue, we found that the methylation level of Tam3 in Antirrhinum is regulated by the Tam3 activity. It is the activity of Tam3, which is dependent on the ability of its transposase to bind DNA, which is affected by growing temperature and the methylation/demethylation of Tam3 is the consequence, not the cause, of transposition.