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Meta heuristics in field environment: improvement of agronomic sustainability and productivity through optimization of soil, weather, and crops

Research Project

Project/Area Number 15KT0038
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeMulti-year Fund
Section特設分野
Research Field Food Cycle Research
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Mochida Keiichi  国立研究開発法人理化学研究所, 環境資源科学研究センター, チームリーダー (90387960)

Co-Investigator(Kenkyū-buntansha) 平山 隆志  岡山大学, 資源植物科学研究所, 教授 (10228819)
最相 大輔  岡山大学, 資源植物科学研究所, 准教授 (90325126)
Research Collaborator Takahagi Kotaro  
Sakurai Tetsuya  
Matsuura Takakazu  
Project Period (FY) 2015-07-10 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥17,810,000 (Direct Cost: ¥13,700,000、Indirect Cost: ¥4,110,000)
Fiscal Year 2018: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2017: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2016: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
Fiscal Year 2015: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000)
Keywordsオオムギ / ゲノム / 機械学習 / ライフコース / トランスクリプトーム / 植物ホルモン / 環境応答
Outline of Final Research Achievements

In this study, we aimed to integrate various physiological data from crops grown under field conditions by transcriptome and hormone analysis throughout their life-course, and to develop a basis for agri-data science to maximize crop productivity and sustainability through computational modeling. For this purpose, we investigated time series transcriptome and hormone datasets from a wild barley and a landrace accession, and revealed physiological changes along with their growth. We also analyzed genome-scale polymorphisms of diverse barley accessions. Moreover, using a legacy dataset of heading date of barely accessions and weather datasets, we developed statistical and/or machine learning-based models that estimate barely heading date.

Academic Significance and Societal Importance of the Research Achievements

地球規模の気候変動と人口の増加により食料供給は多様なリスクに直面している。農地の持続性と作物の生産性の両立が課題である。農地の生産性や持続性は、農地環境と作物の遺伝要因との相互作用によって決まる。本研究では、野外環境で栽培されているオオムギを材料として、栽培の初期から収穫期までの、遺伝子発現や植物ホルモンの状態を成長に沿って調査し、その動態と系統間の違いを明らかにした。また、オオムギの出穂時期を、遺伝子型や遺伝子発現等から推定する方法論の開発を行った。これらの成果は、そょうらいの気候変動に対して予見性をもった作物の育種等の基盤となる技術を提供するものと期待できる。

Report

(5 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (25 results)

All 2019 2018 2017 2016 2015 Other

All Int'l Joint Research (2 results) Journal Article (8 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 8 results,  Open Access: 8 results,  Acknowledgement Compliant: 2 results) Presentation (15 results) (of which Int'l Joint Research: 8 results,  Invited: 6 results)

  • [Int'l Joint Research] Università degli Studi di Trento(イタリア)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] University of Arizona/University of Illinois(米国)

    • Related Report
      2018 Annual Research Report
  • [Journal Article] Statistical and Machine Learning approaches to predict gene regulatory networks from transcriptome datasets2018

    • Author(s)
      K. Mochida, S. Koda, K. Inoue and R. Nishii
    • Journal Title

      Frontiers in Plant Science

      Volume: 9 Pages: 1-8

    • DOI

      10.3389/fpls.2018.01770

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Computer vision-based phenotyping for improvement of plant productivity: a machine learning perspective2018

    • Author(s)
      Mochida Keiichi、Koda Satoru、Inoue Komaki、Hirayama Takashi、Tanaka Shojiro、Nishii Ryuei、Melgani Farid
    • Journal Title

      GigaScience

      Volume: 8 Issue: 1 Pages: 1-12

    • DOI

      10.1093/gigascience/giy153

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Control of seed dormancy and germination by DOG1-AHG1 PP2C phosphatase complex via binding to heme.2018

    • Author(s)
      Nishimura N, Tsuchiya W, Moresco JJ, Hayashi Y, Satoh K, Kaiwa N, Irisa T, Kinoshita T, Schroeder JI, Yates III JR, Hirayama T, Yamazaki T.
    • Journal Title

      Nature Communications

      Volume: 9 Issue: 1 Pages: 2132-2132

    • DOI

      10.1038/s41467-018-04437-9

    • NAID

      120006533266

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The Putative Peptide Gene FEP1 Regulates Iron Deficiency Response in Arabidopsis2018

    • Author(s)
      Hirayama Takashi、Lei Gui Jie、Yamaji Naoki、Nakagawa Naoki、Ma Jian Feng
    • Journal Title

      Plant and Cell Physiology

      Volume: 59 Issue: 9 Pages: 1739-1752

    • DOI

      10.1093/pcp/pcy145

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The mechanism of SO2-induced stomatal closure differs from O3 and CO2 responses and is mediated by nonapoptotic cell death in guard cells2018

    • Author(s)
      Ooi Lia、Matsuura Takakazu、Munemasa Shintaro、Murata Yoshiyuki、Katsuhara Maki、Hirayama Takashi、Mori Izumi C.
    • Journal Title

      Plant, Cell & Environment

      Volume: 42 Issue: 2 Pages: 437-447

    • DOI

      10.1111/pce.13406

    • NAID

      120006769766

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Diurnal Transcriptome and Gene Network Represented through Sparse Modeling in Brachypodium distachyon2017

    • Author(s)
      Koda S, Onda Y, Matsui H, Takahagi K, Uehara-Yamaguchi Y, Shimizu M, Inoue K, Yoshida T, Sakurai T, Honda H, Eguchi S, Nishii R and Mochida K
    • Journal Title

      Front. Plant Sci

      Volume: 8 Pages: 2055-2055

    • DOI

      10.3389/fpls.2017.02055

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley2016

    • Author(s)
      Kotaro Takahagi, Yukiko Uehara-Yamaguchi, TakuhiroYoshida, Tetsuya Sakurai, Kazuo Shinozaki, Keiichi Mochida, Daisuke Saisho
    • Journal Title

      Scientific Reports

      Volume: 6 Issue: 1 Pages: 1-11

    • DOI

      10.1038/srep33199

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Crop improvement using life cycle datasets acquired under field conditions2015

    • Author(s)
      Mochida K, Saisho D, Hirayama T.
    • Journal Title

      Front. Plant Sci.

      Volume: 6 Pages: 740-740

    • DOI

      10.3389/fpls.2015.00740

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] Phenotypic plasticity of barley developmental trajectory2019

    • Author(s)
      Daisuke Saisho, Jun Ito, Hiroyuki Tsuji, Keiichi Mochida, Yoko Ikeda, Takashi Hirayama
    • Organizer
      Phenome 2019 Tucson, AZ, U.S.A.
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Homoeolog-Specific Activation of Genes for Heat Acclimation in Brachypodium hybridum2019

    • Author(s)
      Keiichi Mochida and Jotaro Takahagi
    • Organizer
      Plant and Animal Genome XXVII
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Physiological dynamics across diverse barley accessions under filed condition illustrated by combined hormonome and transcriptome profiling2019

    • Author(s)
      Keiichi Mochida, Komaki Inoue; Yukiko Uehara-Yamaguchi, Minami Shimizu; Kotaro Takahagi; Asaka Kanatani ; Takakazu Matsuura; Daisuke Saisho; Takashi Hirayama
    • Organizer
      Phenome 2019
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Field multi-omics approaches in barley toward robust crop development2018

    • Author(s)
      Daisuke Saisho, Jun Ito, Hiroyuki Tsuji, Keiichi Mochida, Yoko Ikeda, Takashi Hirayama
    • Organizer
      IBMW2018, University of Dundee, Dundee, Scotland
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Functional regression modeling for agricultural data2018

    • Author(s)
      Hidetoshi Matsui and Keiichi Mochida
    • Organizer
      11th International Conference of the ERCIM WG on Computational and Methodological Statistics
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Functional data analysis applied to identify time-series changes of environmental factors that are related to flowering in barley2018

    • Author(s)
      Keiichi Mochida, Hidetoshi Matsui, Kotaro Takahagi, Komaki Inoue, Makoto Ishii, Kazuhiro Sato, Takashi Hirayama
    • Organizer
      第59回日本植物生理学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] An integrated genome information resource in Pooideae and its application to identify homoeologous relations of transcription factors in barley and wheat2018

    • Author(s)
      Komaki Inoue, Kotaro Takahagi, Takashi Hirayama, Keiichi Mochida
    • Organizer
      第59回日本植物生理学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Barley developmental transition and its diversity revealed by field transcriptomics2018

    • Author(s)
      Kotaro Takahagi, Yasuhiro Matsushita, Komaki Inoue, Yukiko Uehara-Yamaguchi, Daisuke Saisho, Satoru Koda, Ryuei Nishii, Takashi Hirayama, Keiichi Mochida
    • Organizer
      第59回日本植物生理学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] A life course approach aiming to design climate-resilient crops2018

    • Author(s)
      Keiichi Mochida
    • Organizer
      九州大学IMIシンポジウム
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 圃場環境下における野生オオムギと栽培オオムギの生長段階と植物ホルモン動態の季節変動2017

    • Author(s)
      最相大輔, 松浦恭和,池田陽子,森泉,持田恵一,平山隆志
    • Organizer
      日本育種学会
    • Place of Presentation
      愛知県名古屋市
    • Year and Date
      2017-03-29
    • Related Report
      2016 Research-status Report
  • [Presentation] オオムギ遺伝資源における圃場出穂期の年次変動要因2017

    • Author(s)
      石井 誠・佐藤和広・持田恵一・高萩航太郎・井上小槙
    • Organizer
      育種学会132回講演会
    • Related Report
      2017 Research-status Report
  • [Presentation] 植物科学とデータ科学を融合したバイオマス増産研究2017

    • Author(s)
      持田恵一
    • Organizer
      近畿バイオ・バイオマスイノベーション研究会
    • Related Report
      2017 Research-status Report
    • Invited
  • [Presentation] Crop design based on life cycle datasets toward sustainable agriculture2017

    • Author(s)
      Keiichi Mochida
    • Organizer
      岡山大学ストレス科学研究シンポジウム
    • Place of Presentation
      岡山県倉敷市
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Advances in omics and bioinformatics for gene discovery in plants2016

    • Author(s)
      持田恵一
    • Organizer
      Plant Genes and “Omics”: Technology Development
    • Place of Presentation
      ウィーン(オーストリア)
    • Year and Date
      2016-02-11
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] オオムギにおける生物地理的代表品種のトランスクリプトーム解析2015

    • Author(s)
      持田恵一、高萩航太郎、山口(上原)由紀子、吉田拓広、櫻井哲也、篠崎一雄、最相大輔
    • Organizer
      DNA鑑定学会
    • Place of Presentation
      発明開館(東京都)
    • Year and Date
      2015-12-09
    • Related Report
      2015 Research-status Report
    • Invited

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Published: 2015-07-14   Modified: 2020-03-30  

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