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Development of a new breeding strategy which enables intensive selection in aquaculture

Research Project

Project/Area Number 21H02279
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 40040:Aquatic life science-related
Research InstitutionThe University of Tokyo

Principal Investigator

Hosoya Sho  東京大学, 大学院農学生命科学研究科(農学部), 助教 (60526466)

Co-Investigator(Kenkyū-buntansha) 矢澤 良輔  東京海洋大学, 学術研究院, 准教授 (70625863)
Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥17,810,000 (Direct Cost: ¥13,700,000、Indirect Cost: ¥4,110,000)
Fiscal Year 2023: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2022: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2021: ¥11,180,000 (Direct Cost: ¥8,600,000、Indirect Cost: ¥2,580,000)
Keywords選抜育種 / 海産魚 / ゲノム比較 / 超保存領域 / ゲノム編集 / 有害変異 / ゲノミックセレクション
Outline of Research at the Start

選抜育種技術はおよそ100年間、「過度な選抜を行わない」ことをセオリーとしてきた。そのために多数の親個体を抱えながらも、世代毎に少しずつしか選抜を進められなかった。これは、近親交配による有害変異の蓄積を避けるためであるが、産業的には大きなデメリットである。そこで、本研究では「有害変異を多く持つ個体を狙って除去することで過度な選抜を可能にする」新規近交系選抜育種法の開発を目指す。本手法が確立されれば、短期間で収益が得られる育種系統を安定的に作り出せると期待される。

Outline of Final Research Achievements

We have attempted to develop a method for detecting deleterious mutations in fish genomes using the chub mackerel (Scomber japonicus) as a model. To identify nonsynonymous substitutions that are potentially deleterious, we constructed a de novo T2T level genome assembly of chub mackerel with gene functional annotation. Using this genome sequence, we have detected polymorphisms in wild chum mackerel individuals. We are now identifying deleterious non-synonymous mutations using SNPeff. The analysis has been delayed due to low commercial catches of the species and other factors.
We are also attempting to estimate the deleterious effects of mutations in the ultra-conserved region within body fish (i.e., Actinopterygii). The number of fish species for which reference sequences are available has increased significantly compared to the original plan, requiring more sequence analysis than expected, so the project has not been completed.

Academic Significance and Societal Importance of the Research Achievements

選抜育種において過度な選抜は禁忌とされるが、産業的には短期的な収益が得られる過度な選抜を伴う新規選抜法の開発への要望が強い。その実現には、集団中から有害変異を持つ個体を除去する必要がある。本研究では、ゲノミックセレクション法と強有害変異を持つ個体の除去を同時に行う養殖魚の新規近交系選抜育種法の開発に取り組む。この手法が確立すれば、短期間で収益を上げられるような小規模な選抜育種が可能となる。また、企業間で遺伝資源の交換を行うことで継続的な改良も可能になると期待される。さらに、ゲノム中の有害変異の特定は野生集団の遺伝的健全性の評価を可能にすることから、資源動態の将来予測も可能にできると期待される。

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • Research Products

    (18 results)

All 2024 2023 2022

All Journal Article (5 results) (of which Peer Reviewed: 1 results,  Open Access: 1 results) Presentation (13 results) (of which Int'l Joint Research: 3 results,  Invited: 1 results)

  • [Journal Article] Heritability and predictive ability for the heterobothriosis resistance and growth performance in the tiger pufferfish Takifugu rubripes fed standard or low fishmeal diets2024

    • Author(s)
      Lin Zijie、Yoshikawa Sota、Hamasaki Masaomi、Kikuchi Kiyoshi、Hosoya Sho
    • Journal Title

      Aquaculture

      Volume: 588 Pages: 740909-740909

    • DOI

      10.1016/j.aquaculture.2024.740909

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] 養殖魚におけるゲノム選抜育種法 その理論と実践,2023

    • Author(s)
      細谷将
    • Journal Title

      アクアネット

      Volume: 12月号 Pages: 33-37

    • Related Report
      2023 Annual Research Report
  • [Journal Article] 選抜育種の発展とゲノム情報を利用した水産育種の世界的動向2023

    • Author(s)
      細谷将
    • Journal Title

      月間養殖ビジネス臨時増刊号

      Volume: 61 Pages: 42-46

    • Related Report
      2023 Annual Research Report
  • [Journal Article] 選抜育種における基礎集団の作り方―アトランとティラピアに学ぶ―2023

    • Author(s)
      菊池潔・細谷将
    • Journal Title

      月間養殖ビジネス臨時増刊号

      Volume: 61 Pages: 36-41

    • Related Report
      2023 Annual Research Report
  • [Journal Article] 養殖における性決定遺伝子情報の利用―全雌、全雄、そして選抜育種―2023

    • Author(s)
      菊池潔・細谷将
    • Journal Title

      月間養殖ビジネス臨時増刊号

      Volume: 61 Pages: 60-64

    • Related Report
      2023 Annual Research Report
  • [Presentation] 養殖魚におけるゲノム選抜育種に関する研究2024

    • Author(s)
      細谷将
    • Organizer
      令和6年度日本水産学会春季大会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Asian Stinging catfish: Constructing the first draft genome and understanding the genetic diversity and sex determination system2024

    • Author(s)
      Taslima Khanam, Christos Palaiokostas, Sho Hosoya,Kiyoshi Kikuchi, Atiqur Rahman, Nittyananda Chandra Das, Sadia Nusrat Sharna, Jesmin Akter, Kaniz Fatema Nur, Mst. Halima Khatun・Sara Momtaj Chowdhury
    • Organizer
      令和6年度日本水産学会春季大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Toward the construction of T2T representative haplotype-resolved reference assemblies of Scomber japonicus2024

    • Author(s)
      Ahammad Kabir, Kiyoshi Kikuchi, Sho Hosoya
    • Organizer
      令和6年度日本水産学会春季大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Stepwise expansion of the nonrecombining region on sex chromosomes through accumulation of chromosomal inversions in Scomber japonicus2024

    • Author(s)
      Ahammad Kabir, Kiyoshi Kikuchi, Sho Hosoya
    • Organizer
      令和6年度日本水産学会春季大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 粘液胞子虫性やせ病耐性トラフグに関する選抜育種の可能性2024

    • Author(s)
      細谷 将・吉川壮太・濱崎将臣・菊池 潔・山田敏之
    • Organizer
      令和6年度日本水産学会春季大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] BLUP 法によるスジアラ体サイズの遺伝率推定2024

    • Author(s)
      宇治督, 山口智史, 藤倉佑治, 三田哲也, 三好花歩, 風藤行紀, 奥澤公一, 細谷 将
    • Organizer
      令和6年度日本水産学会春季大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Low fishmeal diet can modify genetic architecture underlying growth performance and heterobothriosis resistance in the tiger pufferfish Takifugu rubripes2023

    • Author(s)
      Lin Zijie, Yoshikawa Sota, Hamasaki Masaomi, Kikuchi Kiyoshi, Hosoya Sho
    • Organizer
      The 13th Asia Pacific Marine Biotechnology Conference
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 性決定遺伝子コンプレックスの頻繁な転座が性染色体の急速な置換をもたらす2023

    • Author(s)
      菊池潔・Kabir Ahamad・家田梨櫻・遠藤詩織・細谷将
    • Organizer
      第46回日本分子生物学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 低深度ゲノムワイドリシーケンスによるGBS 解析2023

    • Author(s)
      細谷将・矢澤良輔・金子智美・菊池潔
    • Organizer
      令和5年度日本水産学会春季大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] スジアラ Plectropomus leopardus 連鎖地図の作製2023

    • Author(s)
      宇治督・佐野 菜採・安池元重・中村洋路・關野正志・細谷将
    • Organizer
      令和5年度日本水産学会春季大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Repeated translocation of a supergene underlying rapid sex chromosome turnover.2022

    • Author(s)
      6.Kabir A., Ieda R., Hosoya S., Fujikawa D., Atsumi K., Tajima S., Nozawa A., Hirase S., Koyama T., Nakamura O., Kadota M., Nishimura O., Kuraku S., Nakamura Y., Kobayashi H., Toyoda A., Tasumi S., Kikuchi K.
    • Organizer
      Evolution meeting
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] マサバのドラフトゲノムと連鎖地図.2022

    • Author(s)
      細谷将・谷怜央人・矢澤良輔・吉崎悟朗・菊池潔.
    • Organizer
      令和4年度日本水産学会春季大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 2.Kabir A., Kikuchi K., Hosoya S. 2022. A jumping sex-determining locus drove rapid turnover of sex chromosomes in Takifugu pufferfish.2022

    • Author(s)
      Kabir A., Kikuchi K., Hosoya S.
    • Organizer
      XIV International Symposium on Genetics in Aquaculture
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research

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Published: 2021-04-28   Modified: 2025-01-30  

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