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

2023 Fiscal Year Final Research Report

• Project/Area Number: 21H02279
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Review Section: Basic Section 40040:Aquatic life science-related
• Research Institution: The 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
• 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 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.

Free Research Field

魚類遺伝育種学

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。