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

在植物中，通常发现表型变异是由遗传变化引起的。然而，最近有研究表明，由于甲基化状态异常导致的表观遗传变化也可能导致表型变异。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可以遗传地维持。因此，植物基因组片段甲基化状态的改变可能会在后代中传递和维持。本研究包括两个部分来确定甲基化状态可变的基因片段的存在和了解其机制。首先，研究了粳稻、籼稻和野生稻等9个水稻品系中甲基化状态变化的基因组片段。其次，我们分析了Antirrhinum转座子Tam3的去甲基化过程，其活性受到温度的严格控制，似乎与其甲基化状态相关。在第一个问题上，我们的研究结果表明，非多态性片段中表观遗传（epi）标记的出现似乎与9个水稻品系中任意两个品系之间的遗传距离相关。相比之下，在所有对中，表标记占片段总数（包括多态性和非多态性片段）的比例不变（2-3%）。我们假设水稻基因组甲基化的表观遗传差异影响某些表型变异。关于第二个问题，我们发现Antirrhinum中Tam3的甲基化水平受Tam3活性的调节。它是Tam3的活性，它依赖于它的转座酶结合DNA的能力，这受到生长温度的影响，Tam3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.