National Institute of Agricultural Biotechnology (NIAB) Analysis of the rice gene expression profile by 60K microarray Kim Yong-Hwan 1), Lee Jung-Sook, 1) Yoon Ung-Han 1), Lee Kang-Seob 1), Nahm Back-Hie 2), Song Sang-Ik 2), Choi Sang-Bong 2), Ahn Joong-Hoon 3) 1) National Institute of Agricultural Biotechnology, RDA, Suwon, , South Korea 2) Myoung Ji University, Yong In, , South Korea 3) KonKuk University, Seoul, , South Korea   Rice variety : Dong-Jin Byeo   Rice 60K oligomer chip - Rice Whole genome Oligomer Chip - 64,000 spots in two slides - - Design of 70mers with Gene Prediction   Experimental procedure - Dye Labeling - Hybridization - Two dye analysis ; Cy3 (control) and Cy5 (Treatment)   Microarray analysis: - Data capturing with GenePix Pro Data processing with Acuity v Statistical Analysis.   Expressed gene profile of rice - Tissue specific expression (9,768) ; Regeneration tissue ; 790 Flower ; 4,039 Root ; 2,173 Leaf ; 2,766 Transcription factor ; Two fold change by Hormone treatment (3,287) Transcription factor ; 249   Future plan To construct the expression gene network in rice, we will used Ac/Ds mutant lines and transgenic rice as many as possible and the obtained DNA chip data will be opened at NIAB home page (NABIC) Results Rice 60K Oligomer Microarray Tissue and stage specific transcriptome profiling with Rice 60K Microarrary Hierarchical clustering of tissue specific Expression Profiling Hierarchical clustering of transcription factors Treated with five Plant hormones : Hierarchical clustering of Expression Profiling Treated with five Plant hormones Abstract Materials and Methods Conclusion Management system of gene expression profile of rice at NABIC Hierarchical clustering of transcription factors at rice tissues Putative transcription factors in Rice 60K Microarray: 2,528 Number of TFs significantly changed between tissue comparison Hierarchical clustering of significant spots (12,289) were performed. In order to screen of tissue and plant hormone specific genes from rice, 60K oligomer chips were used. 790 regeneration tissue specific, 4,039 flower specific, 2,173 root specific and 2,766 leaf specific genes were isolated. Among the tissue specific expressed genes, 431 genes were identified as transcription factors. High expressed (2 fold up) 3,287 genes treated by Plant hormones (Jasmonic acid, Salicylic acid, Abscisci acid and Methyl jasmonate) were profiled. 249 out of 3,287 genes were identified as transcription factor. All information of expressed gene of rice DB will be opened at NABIC (National Agricultural Biotechnology Information Center) site ( ) 64,904 spots / two slides, 48 blocks of 12 rows and 4 columns. 676 (26x26) spots 60,100 oligomers - Known and predicted genes: 57,734 - Antisense : 2,310 - Randomized control DNA : 66 - Blank spots: 4,190 Average diameter of 120 um. 70mers with average Tm of 68+/-5° C Effective Cost : 10,000 won/gene X 57,000 genes Reg. callus Leaf Etiolated Leaf root Flower After Pollination callus Germina ting seed Flower Before Pollination Heading Leaf Heading Root Reg. callus Callus Hd Lf Rt Reg callus Hierachial Clustering Flower stage specific (4,039) Leaf specific (2,766) Root specific a(2,173) Root specific b(*) Reg. Callus specific (790) Flower specific group (130) Leaf specific group (110) Root specific group (93) Regeneration group (9) ET JASAABA mJA After 1 hr Whole Genes (8000) ET : 1mM ethephon (Ethylene) JA: 100mM jasmonic acid SA : 100mM salicylic acid ABA: 100mM abscisic acid mJA: 100mM methyl jasmonate ET JASAABAmJA Transcription Factors (600) After 1 hr   Popup window shows detailed microarray data   Sample, Labeling, Hybridization, Scan information   Gene expression level check Group 2X Up 2X Down Total ABA ET JA 1, ,102 mJA SA Total 2,284 1,003 3,287 Group 1.6X Up 1.6X Down Total ERF/AP BHLH bZIP C2H C3H Myb Myb- Related NAC WRKY Subtotal Etc 96 Total fold up regulated transcription factors Hormone ABA ET JA mJA SA Toatal TFs WRKY ERF NAC bHLH Total