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

改变甲基化状态的植物基因组片段的鉴定及其对育种性状的影响

• 批准号: 15380001
• 负责人: KISHIMA Yuji
• 金额: $ 10.3万
• 依托单位: HOKKAIDO UNIVERSITY
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (B)
• 财政年份: 2003
• 资助国家: 日本
• 起止时间: 2003 至 2005
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-15380001/
• 关键词: Plant breeding; DNA metrhylation; epigenetic marker; transposable elements; Rice; Antirrhinum majus; Tam3; Demethylation; メチレーション; 温度反応; トランスポゾンレィスプレイ

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.

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。

项目成果

Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome : implications for evolution and integration

从水稻基因组内源性水稻东格罗杆状病毒样序列中重建假定的DNA病毒：对进化和整合的影响

• 发表时间: 2004
• 期刊: BMC Genomics 5
• 作者: 奥野倫子;生田英輔;宮野道雄;宮野道雄;Shin-Nosuke Hashida;生田英輔;Shin-Nosuke Hashida;So Kobayashi;Miwako Takata;Hashida Shinnosuke;Takata Miwako;Kobayashi Sou;Kunii Motoyuki
• 通讯作者: Kunii Motoyuki

植物のゲノムに潜むウイルス-反復配列に秘められたしなやかでしたたかなゲノム、化学と生物 42巻 704-706

隐藏在植物基因组中的病毒 - 隐藏在重复序列中的灵活而强大的基因组，化学与生物学卷 42, 704-706

• 发表时间: 2004
• 作者: F.Cattaneo;M.E.Pasini;J.Intra;M.Matsumoto;F.Briani;M.Hoshi;M.E.Perotti;貴島祐治
• 通讯作者: 貴島祐治

DNA methylation is not necessary for the inactivation of the Tam3 transposition at non-permissive temperature in Antirrhinum

金鱼草中 Tam3 转座在不允许的温度下失活不需要 DNA 甲基化

• 发表时间: 2005
• 期刊: Journal of Plant Physiology (印刷中)
• 作者: 奥野倫子;生田英輔;宮野道雄;宮野道雄;Shin-Nosuke Hashida;生田英輔;Shin-Nosuke Hashida;So Kobayashi;Miwako Takata;Hashida Shinnosuke
• 通讯作者: Hashida Shinnosuke

Genomics of rice : markers as a tool for breeding. Biotechnology in Agriculture and Forestry, vol. 55, Molecular Marker Systems

水稻基因组学：作为育种工具的标记。

• 发表时间: 2004
• 作者: Kishima;Y.;Onishi;K.;Sano;Y.
• 通讯作者: Y.

トランスポゾンを利用した花色関連形質の解析 「植物色素研究法」 植物色素研究会編 225-234

利用转座子分析花色相关性状《植物色素研究方法》植物色素研究会主编225-234

• 发表时间: 2004
• 作者: 貴島祐治;高田美和子;桑原裕之;佐野芳雄
• 通讯作者: 佐野芳雄