Development of expression biomarkers to estimate nutrient conditions

• Project/Area Number: 16H06171
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Plant molecular biology/Plant physiology
• Research Institution: Ryukoku University
• Principal Investigator: Nagano Atsushi 龍谷大学, 農学部, 講師 (00619877)
• Project Period (FY): 2016-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥24,180,000 (Direct Cost: ¥18,600,000、Indirect Cost: ¥5,580,000); Fiscal Year 2018: ¥7,020,000 (Direct Cost: ¥5,400,000、Indirect Cost: ¥1,620,000); Fiscal Year 2017: ¥7,020,000 (Direct Cost: ¥5,400,000、Indirect Cost: ¥1,620,000); Fiscal Year 2016: ¥10,140,000 (Direct Cost: ¥7,800,000、Indirect Cost: ¥2,340,000)
• Keywords: トランスクリプトーム / 栄養 / リン / 発現マーカー / 統計モデリング / 機械学習 / RNA-Seq / バイオマーカー / 環境応答 / 数理工学

Outline of Final Research Achievements

It is important to measure quantity of nutrients in plants for plant science and agriculture. In this study, we develop gene-expression markers to estimate the quantity of nutrients. Low-cost and high-throughput RNA-Seq library preparation system was updated for collecting massive transcriptome data to train the markers. We developed the markers using transcriptome data and trait data of samples in various nutrient conditions, temperature conditions, light conditions and circadian timings.

Academic Significance and Societal Importance of the Research Achievements

本研究で開発した植物の栄養状態を推定する発現マーカーは、作物の栄養状態の診断や適切な施肥タイミングや施肥方法の検討に役立つと考えられる。また、野生植物への応用が可能になった場合には、熱帯林の一斉開花や、ブナの豊凶、地域の植生などを予測するモデルと組み合わせて用いることで、これらの予測の精度を高められる可能性がある。

Research Products

• [Journal Article] Annual transcriptome dynamics in natural environments reveals plant seasonal adaptation (2019)
  • Author(s): Nagano AJ, Kawagoe T, Sugisaka J, Honjo MN, Iwayama K, Kudoh H
  • Journal Title: Nature Plants Volume: 5 Issue: 1 Pages: 74-83
  • DOI: 10.1038/s41477-018-0338-z
  • Peer Reviewed
• [Journal Article] A first genetic map in the genus Streptocarpus generated with RAD sequencing based SNP markers (2018)
  • Author(s): Yun-Yu Chen, Kanae Nishii, Sadie Barber, Christine Hackett, Catherine A. Kidner, Karim Gharbi, Atsushi J. Nagano, Akitoshi Iwamoto, Michael Moeller
  • Journal Title: South African Journal of Botany Volume: 117 Pages: 158-168
  • DOI: 10.1016/j.sajb.2018.05.009
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Broad distribution spectrum from Gaussian to power law appears in stochastic variations in RNA-seq data (2018)
  • Author(s): Awazu Akinori、Tanabe Takahiro、Kamitani Mari、Tezuka Ayumi、Nagano Atsushi J.
  • Journal Title: Scientific Reports Volume: 8 Issue: 1 Pages: 1-8
  • DOI: 10.1038/s41598-018-26735-4
  • NAID: 130007736435
  • Peer Reviewed / Open Access
• [Journal Article] Stacksbinder: online tool for visualizing and summarizing Stacks output to aid filtering of SNPs identified using RAD sequencing (2018)
  • Author(s): Yasugi Masaki、Tezuka Ayumi、Nagano Atsushi J.
  • Journal Title: Conservation Genetics Resources Volume: NA Issue: 1 Pages: 1-3
  • DOI: 10.1007/s12686-018-1050-z
  • Peer Reviewed
• [Journal Article] A Survey on Plant Viruses in Natural Brassicaceae Communities Using RNA-Seq (2018)
  • Author(s): Kamitani M, Nagano AJ, Honjo MN, Kudoh H
  • Journal Title: Microbial Ecology Volume: 24 October Issue: 1 Pages: 1-9
  • DOI: 10.1007/s00248-018-1271-4
  • NAID: 120006647297
  • Peer Reviewed / Open Access
• [Journal Article] Does genomic variation in a foundation species predict arthropod community structure in a riparian forest? (2018)
  • Author(s): Kagiya Shinnosuke、Yasugi Masaki、Kudoh Hiroshi、Nagano Atsushi J.、Utsumi Shunsuke
  • Journal Title: Molecular Ecology Volume: 27(5) Issue: 5 Pages: 1284-1295
  • DOI: 10.1111/mec.14515
  • Peer Reviewed
• [Journal Article] Phylogenetic relationships of Aurantioideae (Rutaceae) based on RAD-Seq (2018)
  • Author(s): Nagano Yukio、Mimura Takashi、Kotoda Nobuhiro、Matsumoto Ryoji、Nagano Atsushi J.、Honjo Mie N.、Kudoh Hiroshi、Yamamoto Masashi
  • Journal Title: Tree Genetics & Genomes Volume: 14 Issue: 1 Pages: 6-6
  • DOI: 10.1007/s11295-017-1223-z
  • Peer Reviewed
• [Journal Article] Phylogeographic analysis of the East Asian goldenrod (Solidago virgaurea complex, Asteraceae) reveals hidden ecological diversification with recurrent formation of ecotypes (2017)
  • Author(s): Sakaguchi Shota、Kimura Takuma、Kyan Ryuta、Maki Masayuki、Nishino Takako、Ishikawa Naoko、Nagano Atsushi J、Honjo Mie N、Yasugi Masaki、Kudoh Hiroshi、Li Pan、Choi Hyeok Jae、Chernyagina Olga A、Ito Motomi
  • Journal Title: Annals of Botany Volume: 121 Issue: 3 Pages: 489-500
  • DOI: 10.1093/aob/mcx182
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Unfolded protein response transducer IRE1-mediated signaling independent of XBP1 mRNA splicing is not required for growth and development of medaka fish (2017)
  • Author(s): Tokiro Ishikawa, Makoto Kashima, Atsushi J Nagano, Tomoko Ishikawa-Fujiwara, Yasuhiro Kamei, Takeshi Todo, Kazutoshi Mori
  • Journal Title: eLife Volume: 6:e26845 Pages: 1-29
  • DOI: 10.7554/elife.26845
  • NAID: 120006358815
  • Peer Reviewed / Open Access
• [Journal Article] First report of Pelargonium zonate spot virus from wild Brassicaceae plants in Japan (2017)
  • Author(s): Kamitani M, Nagano AJ, Honjo MN, Kudoh H
  • Journal Title: Journal of General Plant Pathology Volume: 83 Issue: 5 Pages: 329-332
  • DOI: 10.1007/s10327-017-0727-6
  • NAID: 120006529726
  • Peer Reviewed
• [Presentation] Plant responses to complex natural environments captured by field transcriptomics (2019)
  • Author(s): Atsushi J. Nagano
  • Organizer: 1st ITbM Frontier Seminar
  • Invited
• [Presentation] 境界を越え、異分野に学ぼう～野外トランスクリプトーム研究などを通じて～ (2018)
  • Author(s): 永野惇
  • Organizer: 日本植物学会
  • Invited
• [Presentation] 野外におけるトランスクリプトーム変動を予測する (2018)
  • Author(s): 永野惇
  • Organizer: 第7回生命医薬情報学連合大会
  • Invited
• [Presentation] Genomic dissection and prediction of transcriptome dynamics in field conditions (2018)
  • Author(s): Atsushi J. Nagano
  • Organizer: T-PIRC Symposium
  • Int'l Joint Research / Invited
• [Presentation] 野外環境における植物システムの 包括的設計・制御に向けた基盤技術 (2018)
  • Author(s): 永野惇
  • Organizer: 植物-農業ワークショップ高温・高CO2でも環境負荷の少ない農業を実現する基盤研究
  • Invited
• [Presentation] Genomic dissection and prediction of transcriptome dynamics under fluctuating field conditions (2018)
  • Author(s): Atsushi J. Nagano
  • Organizer: Plant and Animal Genome Conference XXVI
  • Int'l Joint Research / Invited
• [Presentation] Genomic dissection and prediction of transcriptome dynamics under fluctuating field conditions (2018)
  • Author(s): Atsushi J. Nagano
  • Organizer: In natura workshop
  • Int'l Joint Research / Invited
• [Presentation] How transcriptome reflects fluctuations in biotic and abiotic environments in the field (2017)
  • Author(s): 永野惇
  • Organizer: 分子微生物科学セミナー
  • Invited
• [Presentation] Field transcriptomics: Integration of transcriptomics and meteorology (2017)
  • Author(s): Atsushi J. Nagano
  • Organizer: The 33rd annual meeting of the International Society of Chemical Ecology
  • Int'l Joint Research / Invited
• [Presentation] トランスクリプトームによる植物内部状態の推定と栄養研究への応用の可能性 (2017)
  • Author(s): 永野惇
  • Organizer: 第三回植物の栄養研究会
  • Invited
• [Presentation] 野外トランスクリプトミクスでつなぐ、ゲノム、気象、表現型 (2017)
  • Author(s): 永野惇
  • Organizer: 日本作物学会・第243講演会
  • Place of Presentation: 東京大学
• [Presentation] 野外トランスクリプトミクスから分子生物学と農業気象の接点を探る (2017)
  • Author(s): 永野惇
  • Organizer: 日本農業気象学会2017年全国大会
  • Place of Presentation: 北里大学
• [Presentation] 気象とトランスクリプトームの解析からみる野外での植物の温度応答 (2016)
  • Author(s): 永野惇
  • Organizer: Biothermology Workshop - 生命システムの熱科学 -
  • Place of Presentation: 岡崎カンファレンスセンター
• [Presentation] 野外トランスクリプトミクスでつなぐ、ゲノム、気象、表現型 (2016)
  • Author(s): 永野惇
  • Organizer: 2016年植物科学シンポジウム「植物科学とイノベーション」
  • Place of Presentation: 東京大学
• [Book] 定量生物学 (2018)
  • Author(s): 小林 徹也
  • Total Pages: 250
  • Publisher: 化学同人
  • ISBN: 9784759817300
• [Patent(Industrial Property Rights)] トピックモデルを用いた遺伝子情報推定装置 (2017)
  • Inventor(s): 岩山幸治, 永野惇
  • Industrial Property Rights Holder: 岩山幸治, 永野惇
  • Industrial Property Rights Type: 特許
  • Industrial Property Number: 2017-033381
  • Filing Date: 2017