Poster: Bioinformatics

Abs # 857: The Transcriptome Profiling Analysis of Rice Tissues with Rice 60K Oligomeric Microarray Representing Rice Genome Coding Sequences.

Presenter:	Kim, Yeonki , kim750@ggbio.com
Authors	Kim, Yeonki  (A)   Kim, Minjeong  (A)   Kim, Jukon  (B)   Oh, Sejun  (B)   Kang, Kyuyoung  (C)   Kim, Dohoon  (D)   Kang, Sangku  (E)   Galbraith, David  (F)   Kim, Minkyun  (G)   Nahm, Baek Hie  (A)
Affiliations:	(A): GreenGene Biotech Inc. and Division of BioScience and Bioinformatics (B): Division of BioScience and Bioinformatics, Myongji University (C): Dept. of Agriculutral Chemistry, Kyungsang University (D): College of Natural Resources and Life Science, Dong-A University (E): Institute of Biotechnology, Yeungnam University (F): Dept. of Plant Sciences, University of Arizona (G): Division of Applied Biosciences, College of Agriculture, Seoul National University
Web Site:	http://www.ggbio.com

For transciptome profililing, Rice 60K Whole Oligomeric DNA Microarray representing the organism's entire genes was developed. In total, 60,727 oligomers were designed from gene specific regions of both rice subspecies, japonica and indica. These include 58,417 from known and predicted genes, 2,310 antisense sequences and 66 randomized DNA. A set of Rice 60K Microarray composed of two slides with total 64,896 spot addresses including 4,097 blanks. Each oligomers, 70 nt long and average Tm of 78”ĘC, was printed in each spot address with a diameter of 100 um. Whole transcripts from control and treated samples were labelled with Cy3 and Cy5 and hybrized to the oligomer spots. These include germinating seeds in the presence of hormones, 14-day old shoots under high salt (400 mM) stress, regenerating calli, and flowers before and after pollination. For the validation of analysis, the total number of significant spots, ribosomal protein spots, multiple spots and control blank spots were analysed after normalization. The significantly induced or repressed genes with treatment were categorized according to the COG analysis. The total number of signifiantly expressed genes ranged from 16,000 in flowers upto 50,000 in germinating seeds. Gene expressions of about 350 known and putative ribosomal proteins maintained relatively constant through the tissues under the high salt conditions except in the regenerating calli. The massive analysis of gene expression at genome level with the Rice 60K Microarray will accelerate the rice research not only for the understanding of gene expression network, but also for the functional analysis of genes related to important agronomic traits for future environmental agriculture.