Identification of DNA markers and promoters for rice cold tolerancebreeding using SuperSAGE

• Project/Area Number: 18688001
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Breeding science
• Research Institution: Iwate Biotechnology Research Center
• Principal Investigator: MATSUMURA Hideo Iwate Biotechnology Research Center, 生命科学研究部, 主任研究員 (40390885)
• Project Period (FY): 2006 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥29,510,000 (Direct Cost: ¥22,700,000、Indirect Cost: ¥6,810,000); Fiscal Year 2008: ¥9,620,000 (Direct Cost: ¥7,400,000、Indirect Cost: ¥2,220,000); Fiscal Year 2007: ¥9,620,000 (Direct Cost: ¥7,400,000、Indirect Cost: ¥2,220,000); Fiscal Year 2006: ¥10,270,000 (Direct Cost: ¥7,900,000、Indirect Cost: ¥2,370,000)
• Keywords: イネ / 耐冷性 / 花粉 / 遺伝子発現 / SuperSAGE / 次世代DNAシークエンサー / 遺伝子発現解析

Research Abstract

イネ栽培過程において最も強く低温による障害をうける出穂前の葯および花粉におけるSuperSAGE法を用いた網羅的な遺伝子発現解析を試みた。耐冷性の強い品種ひとめぼれと弱い品種ササニシキの穂ばらみ期の植物体を各々28℃および15℃で1日間処理し、各試料の凍結切片から葯組織、花粉を各々レーザーマイクロダイセクション装置を用いて単離し、RNA抽出を行った。抽出したRNAは増幅を行った後にSuperSAGE法による遺伝子発現解析に供試した。これらの試料での解析を行うに当たって近年に急速に進歩した次世代DNAシークエンサーを活用したSuperSAGE法の確立を行った。454社の機器を用いたSuperSAGE法を確立後に花粉等の試料の遺伝子発現解析を実施して10万タグ以上の花粉および葯壁の遺伝子発現情報を収集した。花粉については低温処理区との発現データ比較により低温応答性遺伝子候補を多数見出した。またDNAマーカー探索のために独自にイネインド型品種の全ゲノム配列解析を実施してSNPs情報を収集した。これらの情報を組み合わせて耐冷性プロモーター、マーカーの同を進めている。

Research Products

• [Journal Article] SuperSAGE: The drought stress-responsive transcriptome of chickpea roots (2009)
  • Author(s): Molina C. M. M., Rotter, B., Horres, R., Udupa, S., Besser, B., Bellarmino, L. C., Baum, M., Matsumura, H., Terauchi, R., Kahl, G., Winter, P
  • Journal Title: BMC Genomics 9 Pages: 553-553
  • Peer Reviewed
• [Journal Article] SuperSAGE revealed different classes of early resistance response genes in Capsicum chinense plants harboring L3 -resistance gene infected with Pepper mild mottle virus (2008)
  • Author(s): Hamada, H., Matsumura, H., Tomita, R.,Terauchi, R., Suzuki, K., Kobayashi,K.
  • Journal Title: J. General Plant Pathol 74 Pages: 313-321
  • NAID: 10029716538
  • Peer Reviewed
• [Journal Article] Terauchi SuperSAGE: A modern platform for genome-wide quantitative transcript profiling (2008)
  • Author(s): Matsumura H., Detlev H. Krueger, G.Kahl and R
  • Journal Title: Curr. Pharma. Biotech 9 Pages: 368-374
  • Peer Reviewed
• [Journal Article] Functional genomics in a non-model crop:transcriptomics or proteomics? (2008)
  • Author(s): Carpentier,S.C
  • Journal Title: Physiologia Plantarum 133 Pages: 117-130
  • Peer Reviewed
• [Journal Article] SuperSAGE:A modern platform for genome-wide quantitative transcript profiling. (2008)
  • Author(s): Hideo Matsumura
  • Journal Title: Current Pharmaceutical Biotechnology 9 Pages: 368-374
  • Peer Reviewed
• [Journal Article] SuperSAGE:The drought stress-responsive transcriptome of chickpea roots. (2008)
  • Author(s): Medina, C.M
  • Journal Title: BMC Genomics 9 Pages: 553-553
  • Peer Reviewed
• [Journal Article] SuperSAGEアレイ法 (2008)
  • Author(s): 松村英生
  • Journal Title: 遺伝子医学Mook 10
• [Journal Article] SuperSAGE: A modern platform for genome-wide quantitative transcript profiling (2008)
  • Author(s): Hideo Matsumura
  • Journal Title: Current Pharmaceutical Biotechnology
  • Peer Reviewed
• [Journal Article] SAGE法による耐病性遺伝子発現解析 (2007)
  • Author(s): 松村英生、寺内良平
  • Journal Title: 蛋白質核酸酵素 52 Pages: 660-666
• [Journal Article] High-throughput screen of cell death-inducing factors in Nicotiana benthamiana identifies a novel MAPKK that mediates INF1-induced cell death signaling and non-host resistance to Pseudomonas cichorii (2007)
  • Author(s): Takahashi, Y., Bin Nasir, K. H., Ito, A., Kanzaki, H., Matsumura, H., Saitoh, H., Fujisawa, S., Kamoun, S. and Terauchi, R
  • Journal Title: Plnat J 49 Pages: 1030-1040
  • Peer Reviewed
• [Journal Article] Functional genomics in a non-model crop: transcriptomics or proteomics? (2007)
  • Author(s): Carpentier, S.C., Coemans, B., Podevin, N., Laukens, K., Witters, E., Matsumura, H., Terauchi, R. Swennen, R. Panis, B
  • Journal Title: Phyisol Plant 133 Pages: 117-130
  • Peer Reviewed
• [Journal Article] SAGE法による耐病性遺伝子発現解析 (2007)
  • Author(s): 松村英生
  • Journal Title: 蛋白質核酸酵素 52巻6号 Pages: 660-666
• [Presentation] Digital Gene Expression analysis platform of multiple tissue samples using Next Gen Sequencers (2009)
  • Author(s): Hideo Matsumura
  • Organizer: Next Generation Sequencing
  • Place of Presentation: San Diego,USA
  • Year and Date: 2009-03-17
• [Presentation] Digital Gene Expression analysis platform of multiple tissue samples using Next Gen Sequencers (2009)
  • Author(s): Hideo Matsumura
  • Organizer: Next GenerationSequencing カリフォルニア州
  • Place of Presentation: SanDiego
• [Presentation] イネゲノム育種への次世代シークエンシング技術の活用 (2009)
  • Author(s): 松村英生
  • Organizer: 日本育種学会第115回講演会
  • Place of Presentation: つくば国際会議場
• [Presentation] SuperSAGE: Most advanced transcriptome technology based on 26-bp tag for functional genomics (2007)
  • Author(s): Hideo Matsumura
  • Organizer: Next Generation Sequencing
  • Place of Presentation: Providence(米国、ロードアイランド州)
  • Year and Date: 2007-10-18
• [Presentation] SuperSAGE: Most advanced transcriptome technology based on 26-bp tag for functional genomics. (2007)
  • Author(s): Hideo Matsumura
  • Organizer: Next Generation Sequencing Providence
  • Place of Presentation: 米国、ロードアイランド州
• [Book] Terauchi SuperSAGE Methods in Molecular Biology: vol387 Serial Analysis of Gene Expression 55-70 (Nielsen K.L., Ed.) (2008)
  • Author(s): Matsumura H., Detlev H. Krueger, G. Kahl and R
  • Publisher: HumanaPress
• [Book] The Handbook of Plant Functional Genomics (2008)
  • Author(s): Ryohei Terauchi
  • Total Pages: 576
  • Publisher: WILEY-VCH
• [Book] Methods in Molecular Biology : Serial Analysis of Gene Expression (2007)
  • Author(s): Hideo Matsumura
  • Total Pages: 227
  • Publisher: SuperSAGE
• [Book] SuperSAGE : The most advanced transcriptome technology for functional genomics. Handbook of plant functional genomics
  • Author(s): Terauchi, R., Matsumura, H., Krueger, D. H., Kahl, G. SuperSAGE
  • Publisher: (Kahl, G., Meksam, K. eds) Wiley VCH