Analysis of population genetic structure by environmental DNA and its application to conservation biology

• Project/Area Number: 18K11733
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 64040:Social-ecological systems-related
• Research Institution: Osaka Ohtani University
• Principal Investigator: Uchii Kimiko 大阪大谷大学, 薬学部, 助教 (90469619)
• Project Period (FY): 2018-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2020: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2019: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2018: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
• Keywords: 環境DNA / 交雑 / 保全 / 核DNAマーカー / 一塩基多型 / 交雑集団 / 個体群遺伝構造

Outline of Final Research Achievements

This project used hybridized populations of Japanese native and Eurasian introduced strains of common carp as a model system and developed environmental DNA (eDNA) methods for quantitative analysis of native and non-native allele frequencies at nuclear loci using real-time PCR and high-throughput sequencing. The developed eDNA methods were tested in the field and successfully quantified the native and non-native allele frequencies in the wild population. The estimation from the eDNA methods well corresponded to the results of DNA analyses of carp eggs collected simultaneously with the eDNA samples, indicating the high potential of the eDNA-based methods for rapid assessment of population genetic structure and hybridization.

Academic Significance and Societal Importance of the Research Achievements

本研究では、環境DNA分析が、交雑個体群の遺伝的構造を評価する上で有用なツールとなることを、野外実践を通じて実証することができた。近縁種や同種外来集団の侵入によって引き起こされる在来種との交雑や遺伝子浸透は生物多様性保全において大きな脅威となっているが、本研究で開発したような核DNAマーカーを用いた環境DNA分析による遺伝構造評価法が、その簡便性・迅速性を活かし、交雑や遺伝子浸透の現状把握やスクリーニングのために活用されることが期待される。

Research Products

• [Journal Article] Compilation of real-time PCR conditions toward the standardization of eDNA methods (2021)
  • Author(s): Doi H, Minamoto T, Takahara T, Tsuji S, Uchii K, Yamamoto S, Katano I, Yamanaka H
  • Journal Title: Ecological Research Volume: online first Issue: 3 Pages: 1-10
  • DOI: 10.1111/1440-1703.12217
  • Peer Reviewed
• [Journal Article] An illustrated manual for environmental DNA research: Water sampling guidelines and experimental protocols (2020)
  • Author(s): Minamoto Toshifumi、Miya Masaki、Sado Tetsuya、Seino Satoquo、Doi Hideyuki、Kondoh Michio、Nakamura Keigo、Takahara Teruhiko、Yamamoto Satoshi、Yamanaka Hiroki、Araki Hitoshi、Iwasaki Wataru、Kasai Akihide、Masuda Reiji、Uchii Kimiko
  • Journal Title: Environmental DNA Volume: 3 Issue: 1 Pages: 8-13
  • DOI: 10.1002/edn3.121
  • Peer Reviewed / Open Access
• [Journal Article] Comparison of inhibition resistance among PCR reagents for detection and quantification of environmental DNA. (2019)
  • Author(s): Uchii K, Doi H, Okahashi T, Katano I, Yamanaka H, Sakata KM, Minamoto T.
  • Journal Title: Environmental DNA Volume: 1 Issue: 4 Pages: 359-367
  • DOI: 10.1002/edn3.37
  • Peer Reviewed / Open Access
• [Presentation] 核DNAマーカーを用いた環境DNA分析による交雑レベルの推定 (2020)
  • Author(s): 内井 喜美子
  • Organizer: 日本生態学会第67回大会
• [Presentation] SNPマーカーを用いた環境DNA分析による遺伝変異の検出 (2019)
  • Author(s): 内井喜美子, 土居秀幸, 山中裕樹, 源利文
  • Organizer: 日本生態学会第66回大会
• [Presentation] The use of SNP markers in environmental DNA to detect intraspecific genetic variation (2018)
  • Author(s): Uchii K, Doi H, Yamanaka H, Minamoto T
  • Organizer: 103th ESA Annual Meeting
  • Int'l Joint Research