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Molecular biological analysis of natural mutation occurrence on citrus mutant lines

Research Project

Project/Area Number 24580061
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Horticulture/Landscape architecture
Research InstitutionNational Agriculture and Food Research Organization

Principal Investigator

SHIMIZU Tokurou  国立研究開発法人農業・食品産業技術総合研究機構, 果樹茶業研究部門カンキツ研究領域, 上級研究員 (90355404)

Project Period (FY) 2012-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000)
Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2013: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2012: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywords果樹 / ウンシュウミカン / 突然変異 / 枝変わり / ゲノム解読 / 多型検出 / SNP / INDEL / カンキツ / ゲノム配列 / バイオインフォマティクス / 塩基配列多型 / カラタチ / DNAマーカー
Outline of Final Research Achievements

Mutant selection is an important breeding technology, but the detail of mutation has not been understood. We evaluated whole genome sequences of five satsuma mandarin lines in order to identify the mutation among them. The sequence analysis identified more than 40,000 SNPs and 6,000 indels specific for individual mutant lines. Most of them were found in non-genic region, and observed mutation frequency suggested that replication error of DNA polymerase is a major cause of mutation. DNA markers developed from SNPs or indels located in genic region revealed their stable maintenance in posterior mutant lines, or in nucellar seedlings.These observations suggested frequent occurrence of mutation, but a few of them would substitute normal cell in a tissue, then maintained stably. No obvious increase of mutation detected on nucellar line also suggested that a random selection of existing mutant cells would be the major source of mutant in nucellar seedling.

Report

(5 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • 2012 Research-status Report
  • Research Products

    (11 results)

All 2015 2014 2013 2012

All Journal Article (3 results) (of which Peer Reviewed: 2 results) Presentation (8 results) (of which Invited: 2 results)

  • [Journal Article] Citrus genomics2012

    • Author(s)
      F. G. Gmitter Jr., C. Chen, M. A. Machado, A. A. de Souza, P. Ollitrault, Y. Froehlicher, T. Shimizu
    • Journal Title

      Tree Genetics & Genomes

      Volume: 8 Issue: 3 Pages: 611-626

    • DOI

      10.1007/s11295-012-0499-2

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Genomics approaches for the molecular analysis of citrus mutants2012

    • Author(s)
      T. Shimizu
    • Journal Title

      Gamma Field Symposia

      Volume: 49 Pages: 57-69

    • Related Report
      2012 Research-status Report
  • [Journal Article] カンキツゲノムCGHアレイを利用した温州ミカンの不安定な変異系統とその原系統間での多型性の評価2012

    • Author(s)
      清水徳朗,矢野加奈子,古藤田信博,藤井浩,遠藤朋子,吉岡照高,喜多正幸,寺岡毅
    • Journal Title

      DNA多型

      Volume: 20 Pages: 71-75

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Presentation] Verifying the mandarin breeding: lessons from parentage analysis of citrus varieties2015

    • Author(s)
      清水徳朗、他
    • Organizer
      Plant and Animal Genome XXIII
    • Place of Presentation
      アメリカ、CA、サンディエゴ市
    • Year and Date
      2015-01-10 – 2015-01-14
    • Related Report
      2014 Research-status Report
  • [Presentation] Genome sequence of Satsuma mandarin and comparison to other citrus genome2014

    • Author(s)
      T. Shimizu, Y. Tanizawa, T. Mochizuki, H. Nagasaki, E. Kaminuma, T. Yoshioka, A. Toyoda, A. Fujiyama, Y. Nakamura
    • Organizer
      Plant and Animal Genome XXII
    • Place of Presentation
      San Diego, CA, USA
    • Related Report
      2013 Research-status Report
  • [Presentation] ウンシュウミカンの全塩基配列解読と カンキツのゲノム育種基盤構築への利用2014

    • Author(s)
      清水徳朗
    • Organizer
      園芸学会
    • Place of Presentation
      筑波大学
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] ゲノムワイドSSRマーカー分析によるカラタチおよび関連系統の類縁関係の推定2014

    • Author(s)
      清水徳朗、吉岡照高、喜多正幸、太田智
    • Organizer
      園芸学会
    • Place of Presentation
      筑波大学
    • Related Report
      2013 Research-status Report
  • [Presentation] Whole genome sequencing and DNA marker development in Citrus2013

    • Author(s)
      T. Shimizu
    • Organizer
      第一回韓国果樹ゲノム国際シンポジウム
    • Place of Presentation
      水原市、韓国
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Origin of dwarf, thornless-type trifoliate orange varieties deduced from genome-wide genotyping analysis2012

    • Author(s)
      T. Shimizu, T. Yoshioka, M. Kita, S. Ohta
    • Organizer
      国際柑橘学会第12回大会
    • Place of Presentation
      スペイン・バレンシア市
    • Related Report
      2012 Research-status Report
  • [Presentation] Molecular identification of varieties2012

    • Author(s)
      T. Shimizu
    • Organizer
      国際柑橘学会第12回大会
    • Place of Presentation
      スペイン・バレンシア市
    • Related Report
      2012 Research-status Report
  • [Presentation] Whole genome sequencing and mapping analysis for identifying polymorphism among 11 citrus varieties2012

    • Author(s)
      T. Shimizu, H. Nagasaki, E. Kaminuma, A. Toyoda, A. Fujiyama, Y. Namakura
    • Organizer
      国際柑橘学会第12回大会
    • Place of Presentation
      スペイン・バレンシア市
    • Related Report
      2012 Research-status Report

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Published: 2013-05-31   Modified: 2019-07-29  

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