Digital gene expression QTL analysisas an efficient gene mapping tool

• Project/Area Number: 22380009
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Breeding science
• Research Institution: Shinshu University
• Principal Investigator: MATSUMURA Hideo 信州大学, ヒト環境科学研究支援センター, 准教授 (40390885)
• Project Period (FY): 2010 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥18,460,000 (Direct Cost: ¥14,200,000、Indirect Cost: ¥4,260,000); Fiscal Year 2012: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000); Fiscal Year 2011: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000); Fiscal Year 2010: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000)
• Keywords: ゲノム育種 / 遺伝子発現解析 / DNA マーカー / ゲノム多型 / 遺伝子発現 / 次世代シークエンサー / 連関解析 / イネ / デジタル遺伝子発現解析 / 次世代DNAシークエンサー / 遺伝子発現QTL / Recombinant Inbred Line / 遺伝子型タイピング

Research Abstract

We aimed at developing a novel QTL (quantitative trait locus) mapping procedure based on genome-wide gene expression analysisdata in rice. In the present study, quantitative digital gene expression analysis method was developed, allowed to analyzing expression of thousands of gene in multiple samples, like segregated individuals. Additionally, a novel tool for exploring DNA polymorphisms was also established and it enabled to genotyping many loci at a time. These techniques were basis of digital expression QTL analysis.

Research Products

• [Journal Article] 次世代シーケンサーを利用したタグによる遺伝子発現解析 (2013)
  • Author(s): 松村英生,寺内良平
  • Journal Title: 生物科学 Volume: 64巻 Pages: 151-158
• [Journal Article] SuperSAGE: Powerful Serial Analysis of Gene Expression (2013)
  • Author(s): Matsumura Hideo
  • Journal Title: Methods in Molecular Biology Volume: 883 Pages: 1-17
  • DOI: 10.1007/978-1-61779-839-9_1
  • ISBN: 9781617798382, 9781617798399
  • Peer Reviewed
• [Journal Article] Genome sequencing reveals agronomically important loci in rice using MutMap (2013)
  • Author(s): Abe Akira, Kosugi Shunichi, Yoshida Kentaro, Natsume Satoshi, Takagi Hiroki, Kanzaki Hiroyuki, Matsumura Hideo, (他 7 名 , 7 番 目)
  • Journal Title: Nature Biotechnology Volume: 30 Issue: 2 Pages: 174-178
  • DOI: 10.1038/nbt.2095
  • Peer Reviewed
• [Journal Article] 次世代シーケンサーを利用したタグによる発現解析 (2013)
  • Author(s): 松村英生
  • Journal Title: 生物科学 Volume: 64 Pages: 151-158
• [Journal Article] SuperSAGE : Powerful Serial Analysis of Gene Expression (2012)
  • Author(s): Hideo Matsumura, Naoya Urasaki, Kentaro Yoshida, Detlev H.Kruger, Gunter Kahl, Ryohei Terauchi
  • Journal Title: Method in Molecular Biology Volume: (印刷中) Pages: 883-883
  • Peer Reviewed
• [Journal Article] Cell division and cell elongation in the coleoptile of rice alcohol dehydrogenase 1-deficient mutant are reduced under complete submergence (2011)
  • Author(s): Takahashi H., Saika H., Matsumura H, Nagamura Y., Tsutsumi N., Nishizawa N., Nakazono M.
  • Journal Title: ANNALS OF BOTANY Volume: 108 Issue: 2 Pages: 253-261
  • DOI: 10.1093/aob/mcr137
  • Peer Reviewed
• [Journal Article] A multifaceted genomics approach allows the isolation of the rice Pia-blast resistance gene consisting of two adjacent NBS-LRR protein genes. (2011)
  • Author(s): Okuyama Yudai, Kanzaki Hiroyuki, Abe Akira, Yoshida Kentaro, Tamiru Mlumei, Saitoh Hiromasa, Fujibe Takahiro, Matsumura Hideo,(他 6 名)
  • Journal Title: Plant Journal Volume: 66 Issue: 3 Pages: 467-479
  • DOI: 10.1111/j.1365-313x.2011.04502.x
  • Peer Reviewed
• [Journal Article] High-Throughput SuperSAGE (2011)
  • Author(s): Matsumura Hideo
  • Journal Title: Method in Molecular Biology Volume: 687 Pages: 135-146
  • DOI: 10.1007/978-1-60761-944-4_9
  • ISBN: 9781607619437, 9781607619444
  • Peer Reviewed
• [Journal Article] High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing (2010)
  • Author(s): Matsumura Hideo
  • Journal Title: PLoS ONE 5 Volume: e12010 Issue: 8 Pages: e12010-e12010
  • DOI: 10.1371/journal.pone.0012010
  • NAID: 120007104165
  • Peer Reviewed
• [Journal Article] High-throughput SuperSAGE for digital gene expression analysis of mul tiple samples using next generation sequencing. (2010)
  • Author(s): 松村英生
  • Journal Title: Plos ONE Volume: 5
  • NAID: 120007104165
  • Peer Reviewed
• [Journal Article] High-Throughput SuperSAGE (2010)
  • Author(s): 松村英生
  • Journal Title: Method in Molecular Biology Volume: 687 Pages: 135-146
• [Presentation] RAD-tag 解析法によるイネRecombinant Inbred Lines (RILs) のゲノムワイドな多型解析 (2012)
  • Author(s): 音川俊太郎, 阿部陽, 寺内良平, 松村英生
  • Organizer: 第122回日本育種学会
  • Place of Presentation: 京都
  • Year and Date: 2012-09-14
• [Presentation] RAD-tag解析法によるイネRecombinant Inbred Lines (RILs) のゲノムワイドな多型解析 (2012)
  • Author(s): 音川俊太郎
  • Organizer: 日本育種学会第122回講演会
  • Place of Presentation: 京都産業大学
• [Presentation] タグ配列による網羅的なゲノム多型の解析 (2011)
  • Author(s): 松村英生,阿部陽, 浦崎直也, 宮城徳道, 安藤裕教, 寺内良平
  • Organizer: 第119回日本育種学会
  • Place of Presentation: 横浜
  • Year and Date: 2011-03-29
• [Presentation] タグ配列による網羅的なゲノム多型の解析 (2011)
  • Author(s): 松村英生
  • Organizer: 日本育種学会平成23年春季大会
  • Place of Presentation: 横浜市立大学
• [Book] Tag-based Next Generation Sequencing (2012)
  • Author(s): Matsumura Hideo, Carlos Monina, Detlev H. Kruger, Ryohei Terauchi, Gunter Kahl
  • Publisher: Wiley-Blackwell
• [Book] Tag-based Nex Generation Sequencing (2012)
  • Author(s): Hideo Matsumura
  • Total Pages: 581
  • Publisher: Wiley-Blackwell
• [Book] DeepSuperSAGE : High-Throughput Transcriptome Sequencing with Now- and Next-Generation Sequencing Technologies (Tag-based Nex Generation Sequencing) (2011)
  • Author(s): Hideo Matsumura, Carlos Monina, Detlev H. Kruger, Ryohei Terauchi, Gunter Kahl
  • Publisher: Wiley-VCH