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

Research Project

Project/Area Number 15380001
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Breeding science
Research InstitutionHOKKAIDO UNIVERSITY

Principal Investigator

KISHIMA Yuji  Hokkaido Univ., Grand School of Agr., Asso.Prof, 大学院・農学研究科, 助教授 (60192556)

Co-Investigator(Kenkyū-buntansha) SANO Yoshio  Hokkaido Univ., Grand School of Agr., Prof, 大学院・農学研究科, 教授 (70109528)
Project Period (FY) 2003 – 2005
Project Status Completed (Fiscal Year 2005)
Budget Amount *help
¥16,100,000 (Direct Cost: ¥16,100,000)
Fiscal Year 2005: ¥3,100,000 (Direct Cost: ¥3,100,000)
Fiscal Year 2004: ¥3,100,000 (Direct Cost: ¥3,100,000)
Fiscal Year 2003: ¥9,900,000 (Direct Cost: ¥9,900,000)
KeywordsPlant 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
Research Abstract

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.

Report

(4 results)
  • 2005 Annual Research Report   Final Research Report Summary
  • 2004 Annual Research Report
  • 2003 Annual Research Report
  • Research Products

    (34 results)

All 2006 2005 2004 2003 Other

All Journal Article (26 results) Book (4 results) Patent(Industrial Property Rights) (1 results) Publications (3 results)

  • [Journal Article] The Temperature-dependent change in methylation of the Antirrhinum transposon tam3 is controlled by the activity of its transposase.2006

    • Author(s)
      Hashida, SN., Uchiyama T., Martin C., Kishima Y., Sano Y., Mikami T.
    • Journal Title

      The Plant Cell 18

      Pages: 104-118

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] The temperature-dependent change in methylation of the Antirrhinum transposon tam3 is controlled by the activity of its transposase.2006

    • Author(s)
      Hashida, SN., Uchiyama T., Martin C., Kishima Y., Sano Y., Mikami T.
    • Journal Title

      The Plant Cell 18

      Pages: 104-118

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] The temperature-dependent change in methylation of the antirrhinum transposon Tam3 is controlled by the activity of its transposase2006

    • Author(s)
      Shin-Nosuke Hashida
    • Journal Title

      The Plant Cell 18・1

      Pages: 104-118

    • Related Report
      2005 Annual Research Report
  • [Journal Article] DNA methylation is not necessary for the inactivation of the Tam3 transposon at non-permissive temperature in Antirrhinum.2005

    • Author(s)
      Hashida, SN., Kishima, Y., Mikami, T.
    • Journal Title

      Journal of Plant Physiology 162

      Pages: 1292-1296

    • NAID

      120000953951

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] DNA methylation polymorphisms in rice and wild rice strains : Detection of epigenetic markers2005

    • Author(s)
      Takata, M., Kishima, Y., Sano, Y.
    • Journal Title

      Breeding Science 55

      Pages: 57-63

    • NAID

      110001818712

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Evidence for an evolutionary force that prevents epigenetic silencing between tail-to-tail rice genes with a short spacer2005

    • Author(s)
      Kobayashi, S., Noro, Y., Nagano, H., Yoshida, K.T., Takano-Shimizu, T., Kishima, Y., Sano, Y.
    • Journal Title

      Gene 346

      Pages: 231-240

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] DNA methylation polymorphisms in rice and wild rice strains : Detection of epigenetic markers.2005

    • Author(s)
      Takata, M., Kishima, Y., Sano, Y.
    • Journal Title

      Breeding Science 55

      Pages: 57-63

    • NAID

      110001818712

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Evidence for an evolutionary force that prevents epigenetic silencing between tail-to-tail rice genes with a short spacer.2005

    • Author(s)
      Kobayashi, S., Noro, Y., Nagano, H., Yoshida, K.T., Takano-Shimizu, T., Kishima, Y., Sano, Y.
    • Journal Title

      Gene 346

      Pages: 231-240

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] DNA methylation is not necessary for the inactivation of the Tam3 transposon at non-permissive temperature in Antirrhinum2005

    • Author(s)
      Shin-Nosuke Hashida
    • Journal Title

      Journal of Plant Physiology 162

      Pages: 1292-1296

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Evidence for an evolutionary force that prevents epigenetic silencing between tail-to-tail rice genes with a short spacer2005

    • Author(s)
      So Kobayashi
    • Journal Title

      Gene 346

      Pages: 231-240

    • Related Report
      2005 Annual Research Report
  • [Journal Article] DNA methylation polymorphisms in rice and wild rice strains : detection of epigenetic markers2005

    • Author(s)
      Miwako Takata
    • Journal Title

      Breeding Science 55・1

      Pages: 57-63

    • Related Report
      2005 Annual Research Report
  • [Journal Article] DNA methylation is not necessary for the inactivation of the Tam3 transposition at non-permissive temperature in Antirrhinum2005

    • Author(s)
      Hashida Shinnosuke
    • Journal Title

      Journal of Plant Physiology (印刷中)

    • Related Report
      2004 Annual Research Report
  • [Journal Article] DNA methylation polymorphisms in rice and wild rice strains : detection of epigenetic markers2005

    • Author(s)
      Takata Miwako
    • Journal Title

      Breeding Science 55・1

      Pages: 57-63

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Evidence foran evolutionary force that prevents epigenetic silencing between tail-to-tail rice genes with short spacer2005

    • Author(s)
      Kobayashi Sou
    • Journal Title

      Gene (印刷中)

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome : implications for integration and evolution.2004

    • Author(s)
      Kunii, M., Kanda, M., Nagano, H., Uyeda, I., Kishima, Y., Sano, Y.
    • Journal Title

      BMC Genomics 5

      Pages: 18-18

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Genomics of rice : markers as a tool for breeding. Biotechnology in Agriculture and Forestry.2004

    • Author(s)
      Kishima, Y., Onishi, K., Sano, Y.
    • Journal Title

      Springer-Verlag Berlin Heidelberg Molecular Marker Systems vol.55

      Pages: 245-254

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Virus that was hidden in the plant genomes2004

    • Author(s)
      Kishima, Y.
    • Journal Title

      Kagaku to Seibutsu 42

      Pages: 704-706

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Analysis of the traito association with flower pigmentation by meanings transposon.2004

    • Author(s)
      Kishima, Y., Takata, M., kuwahara, H., Sano, Y.
    • Journal Title

      Syokubutsu Shikiso Kenkyuho

      Pages: 225-234

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Reconstruction of putative DNA virus from endogenous rice tungro bacilliform virus-like sequences in the rice genome : implications for evolution and integration2004

    • Author(s)
      Kunii Motoyuki
    • Journal Title

      BMC Genomics 5

      Pages: 80-80

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Genomics of rice : markers as a tool for breeding2004

    • Author(s)
      Kishima Yuji
    • Journal Title

      Biotechnology in Agriculture and Forestry 55

      Pages: 245-254

    • Related Report
      2004 Annual Research Report
  • [Journal Article] 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植物ゲノム-2004

    • Author(s)
      貴島 祐治
    • Journal Title

      化学と生物 42

      Pages: 704-706

    • Related Report
      2004 Annual Research Report
  • [Journal Article] MITE-transposon display efficiently detects polymorphisms among the Oryza AA-genome species.2003

    • Author(s)
      Takagi, K., Nagano, H., Kishima, Y., Sano, Y.
    • Journal Title

      Breeding Science 53

      Pages: 125-132

    • NAID

      110001803227

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Temperature shift coordinately changes the activity and the methylation state of transposon Tam3 in Antirrhinum majus2003

    • Author(s)
      Hashida, S., Kitamura, K., Mikami T., Kishima, Y.
    • Journal Title

      Plant Physiology 132

      Pages: 1207-1216

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Differentiation of transposon-inducible variegation pattern in crossed lines of snapdragon.2003

    • Author(s)
      Kishima, Y., Ito, Y., Noro, Y., Sano, Y.
    • Journal Title

      Acta Horticulture 612

      Pages: 67-71

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Temperature shift coordinately changes the activity and the methylation state of transposon Tam3 in Antirrhinum majus.2003

    • Author(s)
      Hashida, S., Kitamura, K., Mikami, T., Kishima, Y.
    • Journal Title

      Plant Physiology 132

      Pages: 1207-1216

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Differentiation of transposon-inducible variegation pattern in crossed lines of snapdragon.2003

    • Author(s)
      Kishima, Y., Ito, Y., Noro, Y., Sano.Y.
    • Journal Title

      Acta Horticulture 612

      Pages: 67-71

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Book] 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 704-7062004

    • Author(s)
      貴島祐治
    • Total Pages
      3
    • Publisher
      学会出版センター
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Book] Genomics of rice : markers as a tool for breeding. Biotechnology in Agriculture and Forestry, vol. 55, Molecular Marker Systems2004

    • Author(s)
      Kishima, Y., Onishi, K., Sano, Y.
    • Total Pages
      10
    • Publisher
      Springer-Verlag Berlin Heidelberg
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Book] 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 225-2342004

    • Author(s)
      貴島祐治, 高田美和子, 桑原裕之, 佐野芳雄
    • Total Pages
      10
    • Publisher
      大阪公立大学共同出版会
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Book] 植物色素研究法2004

    • Author(s)
      植物色素研究会編
    • Total Pages
      288
    • Publisher
      大阪公立大学共同出版会
    • Related Report
      2004 Annual Research Report
  • [Patent(Industrial Property Rights)] 核移行に対する阻害活性を有するタンパク質及びこれを用いたタンパク質の核移行制御方法2005

    • Inventor(s)
      貴島祐治, 橋田慎之介, 三上哲夫
    • Industrial Property Rights Holder
      北海道大学長
    • Filing Date
      2005-02-23
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Publications] Takagi Kyoko: "MITE-transposon display efficiently detects polymorphisms among the Oryza AA-genome species"Breeding Science. 53・2. 125-132 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Hashida Shinnosuke: "Temperature shift coordinately changes the activity and the methylation state of transposon Tam3 in Antirrhinum majus"Plant Physiology. 132・3. 1207-1216 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Kishima Yuji: "Differentiation of transposon-inducible variegation pattern in crossed lines of snapdragon"Acta Hort. 612. 67-71 (2003)

    • Related Report
      2003 Annual Research Report

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Published: 2003-04-01   Modified: 2016-04-21  

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