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Analysis of relationship between genetic variation and growth/phenotypic characters of wild Oryza accessions using GWAS

Research Project

Project/Area Number 25252005
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Science in genetics and breeding
Research InstitutionNational Institute of Genetics

Principal Investigator

KURATA Nori  国立遺伝学研究所, 系統生物研究センター, 名誉教授 (90178088)

Co-Investigator(Kenkyū-buntansha) 久保 貴彦  国立遺伝学研究所, 系統生物研究センター, 助教 (00370148)
平井 優美  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 (90415274)
Co-Investigator(Renkei-kenkyūsha) SAWADA Yuji  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, 研究員 (00415176)
Research Collaborator IWATA Hiroyoshi  東京大学, 農学生命科学研究科, 准教授 (00355489)
ONOGI Akio  東京大学, 農学生命科学研究科, 研究員 (60760501)
KANEGAE Hiromi (KAJIYA Hiromi)  東京大学, 農学生命科学研究科, 特任研究員 (30758470)
Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥43,160,000 (Direct Cost: ¥33,200,000、Indirect Cost: ¥9,960,000)
Fiscal Year 2015: ¥14,170,000 (Direct Cost: ¥10,900,000、Indirect Cost: ¥3,270,000)
Fiscal Year 2014: ¥14,170,000 (Direct Cost: ¥10,900,000、Indirect Cost: ¥3,270,000)
Fiscal Year 2013: ¥14,820,000 (Direct Cost: ¥11,400,000、Indirect Cost: ¥3,420,000)
Keywords野生イネ遺伝資源 / ゲノムワイドアソシエーション解析 / メタボローム解析 / アソシエーション解析 / GWAS / 国際研究者交流 / 中国
Outline of Final Research Achievements

Using above 300 accessions of wild Oryza species O. rufipogon, we have investigated relationships between several phenotypic characters such as metabolite, heading date and grain weight, and genetic variation by GWAS analysis. QTL analysis using the crossed population of two strains has also been used for metabolite analysis. The metabolite trigonellin showed the highest QTL peak among 12 positive QTLs of above LOD score 6.0. The GWAS showed a large peak on the same region of the genome and identified two responsible SNPs in the unknown but stress reactive gene as well. To extract candidate SNPs for other phenotypes, we have constructed the SNP-searching database of 400 accessions and continue to detect responsible SNPs.

Report

(4 results)
  • 2016 Final Research Report ( PDF )
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • Research Products

    (16 results)

All 2016 2015 2014 2013 Other

All Int'l Joint Research (2 results) Journal Article (6 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 6 results,  Open Access: 6 results) Presentation (6 results) (of which Int'l Joint Research: 2 results,  Invited: 1 results) Book (1 results) Remarks (1 results)

  • [Int'l Joint Research] 中国科学院(中国)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] 中国科学院(中国)

    • Related Report
      2014 Annual Research Report
  • [Journal Article] OryzaGenome: Genome Diversity Database of Wild Oryza Species2016

    • Author(s)
      Ohyanagi H, Ebata T, Huang X, Gong X, Fujita M, Mochizuki T, Toyoda A, Fujiyama A, Kaminuma E, Nakamura Y, Feng Q, Wang ZX, Han B, Kurata N.
    • Journal Title

      Plant and Cell Physiology

      Volume: 57 Issue: 1 Pages: e1-e1

    • DOI

      10.1093/pcp/pcv171

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Effect of wild and cultivated rice genotypes on rhizosphere bacterial community composition2016

    • Author(s)
      Shenton M, Iwamoto C, Kurata N, Ikeo K.
    • Journal Title

      Rice (N Y)

      Volume: 9 Issue: 1 Pages: 42-42

    • DOI

      10.1186/s12284-016-0111-8

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] RiTE database: a resource database for genus-wide rice genomics and evolutionary biology2015

    • Author(s)
      Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A, Maldonado L CE, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Costa de Oliveira A, Han B, Henry R, Hsing YI, Kurata N, Wang W, Jackson SA, Panaud O, Wing RA.
    • Journal Title

      BMC Genomics

      Volume: 16 Issue: 1 Pages: 538-538

    • DOI

      10.1186/s12864-015-1762-3

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes2015

    • Author(s)
      Horiuchi Y, Harushima Y, Fujisawa H, Mochizuki T, Fujita M, Ohyanagi H, Kurata N.
    • Journal Title

      BMC Genomics

      Volume: 16 Issue: 1 Pages: 1099-1099

    • DOI

      10.1186/s12864-015-2319-1

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] DDBJ Read Annotation Pipeline: a cloud computing-based pipeline for high-throughput analysis of new-generation sequencing data.2013

    • Author(s)
      Nagasaki, H., Mochizuki, T., Kodama, Y., Saruhashi, S., Morizaki, S., Sugawara, H., Ohyanagi, H., Kurata, N., Okubo, K., Takagi, T., Kaminuma, E., Nakamura, Y.
    • Journal Title

      DNA Research

      Volume: 20 Issue: 4 Pages: 383-390

    • DOI

      10.1093/dnares/dst017

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development of INDEL markers to discriminate all genome types rapidly in the genus <i>Oryza</i>2013

    • Author(s)
      Yamaki, S., Ohyanagi, H., Yamazaki, M., Eiguchi, M., Miyabayashi, T., Kubo, T., Kurata, N., Nonomura, K-I.
    • Journal Title

      Breeding Science

      Volume: 63 Issue: 3 Pages: 246-254

    • DOI

      10.1270/jsbbs.63.246

    • NAID

      10031191386

    • ISSN
      1344-7610, 1347-3735
    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] DNA Polymorphism Database from New-Generation Sequence Read Archive and Analytical Workflow2015

    • Author(s)
      Mochizuki, T., Tanizawa, Y., Fujisawa, T., Nikoh, N., Toyoda, A., Fujiyama, A., Kurata, N., Nagasaki, H., Shimizu, T., Kaminuma, E., Nakamura, Y.
    • Organizer
      Plant & Animal Genome XXⅢ
    • Place of Presentation
      San Diego(USA)
    • Year and Date
      2015-01-14
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Consideration of O. rufipogon Diversity with a SNP Database2015

    • Author(s)
      Ohyanagi, H., Ebata, T., Huang X., Gong, H., Fujita, M., Toyoda, A., Fujiyama, A., Wang ZX., Han, B., Yamazaki, Y., Kurata, N.
    • Organizer
      Plant & Animal Genome XXⅢ
    • Place of Presentation
      San Diego(USA)
    • Year and Date
      2015-01-12
    • Related Report
      2014 Annual Research Report
    • Int'l Joint Research
  • [Presentation] メタボロミクスを利用した環境応答の解析と育種への応用利用2014

    • Author(s)
      澤田有司
    • Organizer
      日本育種学会 第126回講演会 第56回シンポジウム 作物環境応答の網羅的計測とモデリング~その育種への活用~
    • Place of Presentation
      南九州大学(宮崎県都城市)
    • Year and Date
      2014-09-26
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] イネ雑種不稔遺伝子S35とEFSの遺伝的関係について2014

    • Author(s)
      久保貴彦、吉村淳、倉田のり
    • Organizer
      日本育種学会第125回講演会
    • Place of Presentation
      東北大学(宮城県仙台市)
    • Year and Date
      2014-03-22
    • Related Report
      2013 Annual Research Report
  • [Presentation] Integrated metabolomics for large scale rice bioresources2014

    • Author(s)
      Sawada, Y., Sato, M., Yamada, Y., Sakata, A., Kurata, N., Hirai, M.Y.
    • Organizer
      Plant and Animal Genome XII
    • Place of Presentation
      Town and Country Hotel(San Diego, USA)
    • Year and Date
      2014-01-13
    • Related Report
      2013 Annual Research Report
  • [Presentation] Diversity of cysteine-rich antimicrobial-like peptides in some Oryza AA genome species2013

    • Author(s)
      Shenton, M., Ohyanagi, H., Toyoda, A., Fujiyama, A., Nagata, T., Kurata, N.
    • Organizer
      11th International Symposium on Rice Functional Genomics
    • Place of Presentation
      The Grand New Delhi(New Delhi, India)
    • Year and Date
      2013-11-23
    • Related Report
      2013 Annual Research Report
  • [Book] 生物の科学 遺伝「栽培イネの起源に迫る」2013

    • Author(s)
      久保貴彦、倉田のり
    • Publisher
      エヌ・ティー・エス
    • Related Report
      2013 Annual Research Report
  • [Remarks] OryzaGenome(本研究に使用した450系統に関するゲノムSNP情報データベース)

    • URL

      http://viewer.shigen.info/oryzagenome/mapview/Top.do

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report

URL: 

Published: 2013-05-15   Modified: 2018-03-22  

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