Development of forest paleogenetic approaches using ancient pollen grains found in an ice core from mountain glacier

• Project/Area Number: 24248025
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Forest science
• Research Institution: Tohoku University
• Principal Investigator: Suyama Yoshihisa 東北大学, (連合)農学研究科(研究院), 准教授 (60282315)
• Co-Investigator(Renkei-kenkyūsha): NAKAZAWA Fumio 大学共同利用機関法人情報・システム研究機構, 新領域融合研究センター, 融合プロジェクト特任研究員 (80432178) ; MAKINO Takashi 東北大学, 生命科学研究科, 准教授 (20443442)
• Research Collaborator: MATSUKI Yu 東北大学, 大学院農学研究科, 研究支援者
• Project Period (FY): 2012-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥44,980,000 (Direct Cost: ¥34,600,000、Indirect Cost: ¥10,380,000); Fiscal Year 2015: ¥8,710,000 (Direct Cost: ¥6,700,000、Indirect Cost: ¥2,010,000); Fiscal Year 2014: ¥8,710,000 (Direct Cost: ¥6,700,000、Indirect Cost: ¥2,010,000); Fiscal Year 2013: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000); Fiscal Year 2012: ¥18,980,000 (Direct Cost: ¥14,600,000、Indirect Cost: ¥4,380,000)
• Keywords: 古代DNA / 遺伝的多様性 / 花粉分析 / 次世代シーケンサー / アイスコア / 集団遺伝 / 分子系統地理 / 針葉樹

Outline of Final Research Achievements

We developed basic methods for paleogenetic approaches using conifer pollen grains found in a mountain glacier. First, we developed a protocol for single-pollen DNA analysis using whole-genome amplification (WGA) method. Second, we developed a novel approach that we termed “multiplexed ISSR genotyping by sequencing” (MIG-seq), which is a PCR-based procedure for constructing highly reduced representation libraries involving de novo SNP discovery, and their genotyping using next generation sequencing. Then we applied these methods to pollen samples found in a glacier.

Research Products

• [Int'l Joint Research] ウプサラ大学(スウェーデン)
• [Journal Article] MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform (2015)
  • Author(s): Yoshihisa Suyama, Yu Matsuki
  • Journal Title: Scientific Reports Volume: 5 Issue: 1
  • DOI: 10.1038/srep16963
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA (2015)
  • Author(s): Laura Parducci, Minna Valiranta, J. Sakari Salonen, Tiina Ronkainen, Irina Matetovici, Sonia L. Fontana, Tiina Eskola, Pertti Sarala, Yoshihisa Suyama
  • Journal Title: Philosophical Transactions of the Royal Society B Volume: 370 Issue: 1660 Pages: 20130382-20130382
  • DOI: 10.1098/rstb.2013.0382
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] 生物地理学とその関連分野における地理情報システム技術の基礎と応用 (2014)
  • Author(s): 岩崎貴也・阪口翔太・横山良太・高見泰興・大澤剛士・池田紘士・陶山佳久
  • Journal Title: 日本生態学会誌 Volume: 64 Pages: 183-199
  • NAID: 110009892536
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Molecular and pollen-based vegetation analysis in lake sediments from central Scandinavia (2013)
  • Author(s): Laura Parducci, Irina Matetovici, Sonia L. Fontana, K.D. Bennett, Yoshihisa Suyama, James Haile, Kurt H. Kjaer, Nicolaj Krog Larsen, Andreas D. Drouzas, Eske Willerslev
  • Journal Title: Molecular Ecology Volume: 22 Issue: 13 Pages: 3511-3524
  • DOI: 10.1111/mec.12298
  • Peer Reviewed
• [Journal Article] DNA analysis for section identification of individual Pinus pollen grains from Belukha glacier, Altai Mountains, Russia (2013)
  • Author(s): Fumio Nakazawa, Jun Uetake, Yoshihisa Suyama, Ryo Kaneko, Nozomu Takeuchi, Koji Fujita, Hideaki Motoyama, Satoshi Imura, Hiroshi Kanda
  • Journal Title: Environ. Res. Lett. Volume: 8 Issue: 1 Pages: 14-32
  • DOI: 10.1088/1748-9326/8/1/014032
  • Peer Reviewed
• [Presentation] Potential of paleogenomics on plant species by using pollen in ice cores (2016)
  • Author(s): Fumio Nakazawa, Yoshihisa Suyama, Satoshi Imura, Hideaki Motoyama
  • Organizer: 日本地球惑星科学連合大会2016
  • Place of Presentation: 幕張メッセ（千葉県千葉市）
  • Year and Date: 2016-05-22
• [Presentation] ingle-pollen genotyping using the next-generation sequencing (2016)
  • Author(s): Yoshihisa Suyama, Yu Matsuki, Fumio Nakazawa
  • Organizer: The 13th International Symposium on Integrated Field Science: Conservation and Utilization of Biodiversity
  • Place of Presentation: 東北大学大学院農学研究科（宮城県仙台市）
  • Year and Date: 2016-03-09
  • Int'l Joint Research
• [Presentation] DNA分析によるベルーハ氷河（アルタイ山脈・ロシア）中のマツ属花粉の種同定 (2015)
  • Author(s): 中澤文男，陶山佳久，伊村智，本山秀明
  • Organizer: 第6回極域科学シンポジウム
  • Place of Presentation: 国立極地研究所（東京都立川市）
  • Year and Date: 2015-11-19
• [Presentation] 南極雪試料中の花粉DNA分析 (2015)
  • Author(s): 中澤文男，陶山佳久，伊村智，本山秀明
  • Organizer: 雪氷研究大会（2015･松本）
  • Place of Presentation: 信州大学理学部（長野県松本市）
  • Year and Date: 2015-09-13
• [Presentation] 全ゲノム増幅法を用いたベルーハ氷河（アルタイ山脈・ロシア）中のマツ属花粉の種同定 (2015)
  • Author(s): 中澤文男，陶山佳久，伊村智，本山秀明
  • Organizer: 雪氷研究大会（2015･松本）
  • Place of Presentation: 信州大学理学部（長野県松本市）
  • Year and Date: 2015-09-13
• [Presentation] An effective PCR-based method for genome-wide SNP genotyping using NGS platform (2015)
  • Author(s): Yoshihisa Suyama, Yu Matsuki
  • Organizer: 11th Clonal Plant Workshop (Clone 2015)
  • Place of Presentation: Institute of Botany of the Czech Academy of Sciences (トジェボニ, Czech Republic)
  • Year and Date: 2015-08-04
  • Int'l Joint Research
• [Presentation] Species identification of Pinus pollen found in a glacier using a whole genome amplification method (2015)
  • Author(s): Fumio Nakazawa, Yoshihisa Suyama, Satoshi Imura, Hideaki Motoyama
  • Organizer: 国際第四紀学会第19回大会
  • Place of Presentation: 名古屋国際会議場（愛知県名古屋市）
  • Year and Date: 2015-07-26
  • Int'l Joint Research
• [Presentation] MIG-seq: an effective PCR-based method for genome-wide SNP genotyping using NGS platform (2015)
  • Author(s): Yoshihisa Suyama
  • Organizer: Workshop of Young Scientists on Biodiversity and Conservation Biology in Southwest China: Advances in Conservation Genetics
  • Place of Presentation: Laboratory of Biodiversity in Southwest China (Kunming, China)
  • Year and Date: 2015-07-10
  • Int'l Joint Research / Invited
• [Presentation] 次世代シーケンサーを用いた山岳氷河中樹木花粉のDNA分析 (2015)
  • Author(s): 松木悠、中澤文男、陶山佳久
  • Organizer: 第62回日本生態学会大会
  • Place of Presentation: 鹿児島大学郡元キャンパス（鹿児島県鹿児島市）
  • Year and Date: 2015-03-18 – 2015-03-22
• [Presentation] Development of a novel method for conservation genetics with next-generation sequencing: Multiplexed ISSR (inter-simple sequence repeat) Genotyping by sequencing (MIG-seq) (2015)
  • Author(s): Yoshihisa Suyama, Yu Mastuki
  • Organizer: Contribution of Genetics to Plant Conservation: International Seminar in Rio de Janeiro Botanical Garden
  • Place of Presentation: Rio de Janeiro Botanical Garden（リオデジャネイロ、ブラジル）
  • Year and Date: 2015-02-06
  • Invited
• [Presentation] Development of a novel method for conservation genetics with next-generation sequencing: Multiplexed ISSR (inter-simple sequence repeat) Genotyping by sequencing (MIG-seq) (2015)
  • Author(s): Yoshihisa Suyama, Yu Mastuki
  • Organizer: Contribution of Genetics to Plant Conservation: Brazil-Japan International Workshop 2015
  • Place of Presentation: University of Sao Paulo（サンパウロ、ブラジル）
  • Year and Date: 2015-02-02 – 2015-02-04
  • Invited
• [Presentation] 全ゲノム増幅法を用いた氷河中の花粉の同定 (2014)
  • Author(s): 中澤文男, 陶山佳久, 伊村智, 本山秀明
  • Organizer: 第5回極域科学シンポジウム
  • Place of Presentation: 国立極地研究所（東京都立川市）
  • Year and Date: 2014-12-02 – 2014-12-05
• [Presentation] 全ゲノム増幅法を用いた氷河中の花粉1粒ずつの同定 (2014)
  • Author(s): 中澤文男, 陶山佳久, 伊村智, 本山秀明
  • Organizer: 日本地球惑星科学連合2014年大会
  • Place of Presentation: パシフィコ横浜 会議センター（神奈川県横浜市）
  • Year and Date: 2014-04-28 – 2014-05-02
• [Presentation] 次世代DNAシーケンシングによる森林分子生態学的研究 (2014)
  • Author(s): 陶山佳久
  • Organizer: 第125回日本森林学会大会
  • Place of Presentation: 大宮ソニックシティー
• [Presentation] 氷河中の花粉1粒ずつの全ゲノム増幅 (2013)
  • Author(s): 中澤文男, 陶山佳久
  • Organizer: 第4回極域科学シンポジウム
  • Place of Presentation: 国立極地研究所
• [Presentation] Whole genome amplification法による氷河中の花粉一粒ずつのゲノムDNA増幅 (2013)
  • Author(s): 中澤文男, 陶山佳久
  • Organizer: 雪氷研究大会（2013･北見）
  • Place of Presentation: 北見工業大学
• [Presentation] 山岳アイスコアから得られた樹木花粉のDNA分析 (2013)
  • Author(s): 松木悠、陶山佳久
  • Organizer: 日本生態学会東北地区会第58回大会
  • Place of Presentation: 星と森のロマントピア（弘前市）
• [Presentation] DNA analysis for section identification of a pine pollen grain from the Belukha glacier, Altai Mountains, Russia (2013)
  • Author(s): Fumio Nakazawa
  • Organizer: Third International Symposium on the Arctic Research
  • Place of Presentation: 日本科学未来館
• [Presentation] ベルーハ氷河中のマツ属花粉１粒ずつのDNA分析によって明らかになった花粉の長距離輸送 (2012)
  • Author(s): 中澤文男
  • Organizer: 第35回極域気水圏シンポジウム
  • Place of Presentation: 国立極地研究所
• [Presentation] ベルーハ氷河中のマツ属花粉１粒ずつのDNA分析から導き出された花粉長距離輸送の可能性 (2012)
  • Author(s): 中澤文男
  • Organizer: 雪氷研究大会（2012･福山）
  • Place of Presentation: 福山市立大学
• [Presentation] DNA analysis for identification of a Pinus pollen grain at subsection level from the Belukha glacier, Altai Mountains, Russia (2012)
  • Author(s): Fumio Nakazawa
  • Organizer: 13th International Palynological Congress and 9th International Organisation of Palaeobotany Conference - IPC/IOPC 2012
  • Place of Presentation: 中央大学
• [Presentation] 亜節レベルでの同定を目的としたベルーハ氷河中のマツ属花粉1粒ずつのDNA分析 (2012)
  • Author(s): 中澤文男
  • Organizer: 日本地球惑星科学連合大会
  • Place of Presentation: 幕張メッセ国際会議場
• [Book] Eco-evolutionary genomic observation for local and global environmental changes. In: S.-i. Nakano et al. (eds.) Integrative Observations and Assessments, Ecological Research Monographs (2014)
  • Author(s): Shin-Ichi Morinaga, Takaya Iwasaki, Yoshihisa Suyama
  • Total Pages: 431
  • Publisher: Springer