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Analysis of genealogy and genome admixture of indigenous citrus varieties by statistical genetics analysis

Research Project

Project/Area Number 18K05634
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 39030:Horticultural science-related
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, 上級研究員 (90355404)

Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2020)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2020: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2019: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords果樹 / カンキツ / 育種 / 系譜 / DNAマーカー / 多型 / ゲノム / バイオインフォマティクス / DNAマーカー分析 / ゲノム解析 / 栽培化 / 遺伝資源 / 遺伝子型 / 遺伝的多様性 / 親子関係 / 遺伝 / 品種分化
Outline of Final Research Achievements

We confirmed citrus varieties' genetic identity, including Natsumikan, and found novel parent-child pedigrees from the comprehensive genotyping of more than 2,000 native citrus varieties. A survey of native Tachibana strains in Japan confirmed that individuals are maintained as clones in their native colony and then identified 11 Tachibana lines, including eight new lines. Based on the genetic similarity and geographical distribution of these Tachibana strains, we found that Tachibana emerged mainly in Miyazaki prefecture and confirmed that Tachibana-B is the Yamato Tachibana. To integrate the revealed pedigree for citrus breeding, we established a method for extracting genome-wide polymorphisms, proposed a novel method, "Citrus breeding 2.0" that avoids the limitations of conventional breeding, and launched a genome-wide polymorphism estimation method using GRAS-Di.

Academic Significance and Societal Importance of the Research Achievements

遺伝子型をもとにカンキツの品種、系統の同一性を示すことで、品種異名の混乱を回避することが可能となった。また、従来一つとされてきたタチバナで11の系統が確認され、それらの発生地が宮崎県と推定されたことや、ヤマトタチバナを特定することができたことで、カンキツ研究に新ページを開いただけでなく、人文や歴史研究の深化にも貢献する。また、解明された系譜とゲノム情報を統合することで従来のカンキツ育種の制約の回避と効率化が可能となる。ゲノムワイド多型を利用して形質予測精度を向上する手法の開発にも着手し、カンキツを始めとする育種を効率化する。

Report

(4 results)
  • 2020 Annual Research Report   Final Research Report ( PDF )
  • 2019 Research-status Report
  • 2018 Research-status Report
  • Research Products

    (9 results)

All 2021 2020 2019 2018

All Journal Article (5 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 5 results,  Open Access: 2 results) Presentation (2 results) Book (2 results)

  • [Journal Article] General Utilities for Genotyping Study (GUGS): A Comprehensive Application in Genotype and Sequence Data Manipulation2021

    • Author(s)
      Shimizu, T
    • Journal Title

      JARQ: Japan Agricultural Research Quarterly

      Volume: 55(2)

    • NAID

      130008112930

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Markers, Maps, and Marker-Assisted Selection2020

    • Author(s)
      Shimizu Tokurou、Aka Kacar Y?ld?z、Cristofani-Yaly Mari?ngela、Curtolo Maiara、Machado Marcos Antonio
    • Journal Title

      The Citrus Genome (Gentile A, La Malfa S and Deng Z eds.)

      Volume: 7 Pages: 107-139

    • DOI

      10.1007/978-3-030-15308-3_7

    • ISBN
      9783030107994, 9783030153083
    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] 静岡県沼津市戸田の自生タチバナ群落の多様性解析とその維持機構の推定2020

    • Author(s)
      清水徳朗、長倉建治、奥田薫樹、稲木博文、奥田勇、遠藤重由
    • Journal Title

      園芸学研究

      Volume: 19 Pages: 141-149

    • NAID

      130007866838

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A model for the domestication and diversification processes of modern citrus cultivars in Japan2019

    • Author(s)
      Shimizu T.、Kitajima A.、Nonaka K.、Yoshioka T.、Ohta S.、Goto S.、Kaminuma E.、Nakamura Y.
    • Journal Title

      Acta Horticulturae

      Volume: 1230 Issue: 1230 Pages: 7-14

    • DOI

      10.17660/actahortic.2019.1230.2

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Determining the parental combinations of the triploid acid citrus cultivars ‘Yellow Bell’ and ‘Tahiti lime’ using DNA marker analyses2019

    • Author(s)
      Nakano Michiharu, Shimizu Tokurou(CA), Sugawa Shun,Kaneyoshi Junko, Kita Masasyuki, Yoshioka Terutaka, Kitajima Akira
    • Journal Title

      Scientia Horticulturae

      Volume: 246 Pages: 893-897

    • DOI

      10.1016/j.scienta.2018.11.071

    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Presentation] 静岡県沼津市戸田の自生タチバナ群落の多様性解析とその維持機構の推定2020

    • Author(s)
      清水徳朗、長倉建治、奥田薫樹、稲木博文、奥田勇、遠藤重由
    • Organizer
      園芸学会2020年春季大会
    • Related Report
      2019 Research-status Report
  • [Presentation] 在来カンキツ品種の来歴と系譜から推定した日本における多様性拡大と栽培化のモデル2018

    • Author(s)
      清水徳朗・北島宣・野中圭介・吉岡照高・太田智・後藤新悟・神沼英理・中村保一
    • Organizer
      園芸学会平成30年度秋季大会
    • Related Report
      2018 Research-status Report
  • [Book] 果樹 vol.12 主要品種の来歴と栽培化の過程2019

    • Author(s)
      農文協編
    • Total Pages
      220
    • Publisher
      農山漁村文化協会
    • ISBN
      9784540190551
    • Related Report
      2019 Research-status Report
  • [Book] 果樹 vol.12 国内での品種伝搬と在来品種の多様性拡大2019

    • Author(s)
      農文協編
    • Total Pages
      220
    • Publisher
      農山漁村文化協会
    • ISBN
      9784540190551
    • Related Report
      2019 Research-status Report

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Published: 2018-04-23   Modified: 2022-12-28  

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