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

• Project/Area Number: 25252005
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Science in genetics and breeding
• Research Institution: National 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: ¥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.

Research Products

• [Int'l Joint Research] 中国科学院(中国)
• [Int'l Joint Research] 中国科学院(中国)
• [Journal Article] OryzaGenome: Genome Diversity Database of Wild Oryza Species (2016)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Effect of wild and cultivated rice genotypes on rhizosphere bacterial community composition (2016)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] RiTE database: a resource database for genus-wide rice genomics and evolutionary biology (2015)
  • 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
  • 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 genes (2015)
  • 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
  • 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
  • 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
  • Peer Reviewed / Open Access
• [Presentation] DNA Polymorphism Database from New-Generation Sequence Read Archive and Analytical Workflow (2015)
  • 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
  • Int'l Joint Research
• [Presentation] Consideration of O. rufipogon Diversity with a SNP Database (2015)
  • 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
  • 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
  • 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
• [Presentation] Integrated metabolomics for large scale rice bioresources (2014)
  • 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
• [Presentation] Diversity of cysteine-rich antimicrobial-like peptides in some Oryza AA genome species (2013)
  • 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
• [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
• [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