Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Expressed Sequence Tags And Transcriptome Analysis Of Brassica rapa

Yoonkang Hur¹ , Myung-Ho Lim² , Jungyeo Lee¹ , Jin-A Kim² , Ho-Il Kim² , Chae Oh Lim³ , Yong-Yoon Chung⁴ , Baek-Hie Nahm⁵ , Yong-Pyo Lim¹ , Beom-Seok Park²

¹  Genome Research Center, Chungnam National University,Daejon 305-764, Korea

²  Brassica Genomics Team, National Institute of Agricultural Biotechnology, Suwon 441-707, Korea

³  Environmental Biotechnology National Core Research Center, Gyeongsang Univ., Jinju, Korea

⁴  School of life Science & Biotechnology, Korea University, Seoul 136-701, Korea

⁵  GreenGene Bio Tech Inc., Myungji University, Youngin 449-728, Korea

A set of 100,000 EST sequences was analyzed from over 20 cDNA libraries of Brassica rapa ssp. pekinensis (Chiifu inbred, reference line of Chinese cabbage for The Multinational Brassica Genome Project). Major cDNA libraries were constructed from tissues or organs in diverse developmental stages, exposed to NaCl and cold temperature, and developing calli on the regeneration medium. These ESTs were clustered and assembled using megablast-Cap3 and produced a set of 12,298 tentative contigs and 11,576 singleton sequences. This set of 23,874 unigenes would be an un-biased collection of ~50% of Brassica genes (ca. 45,000 genes) and cover ~75% of the CDS of Arabidopsis genomes. About 90% and 82% of Brassica unigenes are found to match counter-part with Arabidopsis and rice, respectively, in the criteria of E-30 (blastx). From the blastn (E-08) analysis, genes of B. rapa showed ~84% and ~95% sequence identities with Arabidopsis and B. napus, respectively. In-silico localization of Brassica unigenes onto the Arabidopsis chromosomes resulted in 23.3%, 13.1%, 18.4%, 13.9%, and 20.1% of localized genes onto the chromosome 1 through 5 of Arabidopsis, respectively. Based on the EST sequence information, oligo probes of 23,000 B. rapa unigenes were fabricated and quality of the chip was tested. We will discuss transcription profiles obtained from the Brassica chip analysis with respect to development of Chinese cabbage as well as different Brassica species. [This work was supported by grants from BioGreen21 Progarm and Brassica Genomics Research of NIAB, Rural Development Administration, Republic of Korea]