Poster: Genomics Resources

Abs # 934: BAC end sequence analysis of Chinese cabbbage

Presenter:	Lim, Yong Pyo , yplim@cnu.ac.kr
Authors	Lim, Yong Pyo  (A)   Choi, Su Ruyn  (A)   Hong, Chang Pyo  (A)   Park, Young Soo  (A)
Affiliations:	(A): Department of Horticulture and Genome Research Center

A total of 1,607 non-redundant Chinese cabbage (Brassica rapa L. spp pekinensis) BAC end sequences (BESs), with an average read length of 327 bp based on QV 20, from both ends of 1,386 KBrH clones were generated to evaluate the preliminary sequence-tagged connector (STC) framework for genome sequencing and survey the genetic resources. In comparison between Chinese cabbage BESs and BAC contigs for STC framework, 93 BAC contigs, containing 132 BAC clones applied BESs and covering 1.7% (9.6 Mb) of genome, were searched. Genetic resources were also investigated variously; 11.2% transposable elements (76.8% retrotransposons and 23.2% DNA transposons), 2.4% simple sequence repeats (SSRs), 1.2% orthologous EST contents, and 28.1% protein coding regions (associated with 73.1% molecular function, 12% biological process, and 14.9% cellular component), and the 6 SSR markers were developed by identifying polymorphisms among mapping population. In comparison for coding regions between Chinese cabbage BESs and Arabidopsis based on a cutoff expectation value of <10^-5, 84% of protein coding regions of Chinese cabbage BESs were homologue to that of Arabidopsis. From these results, we suggest that BES may be a useful tool for selecting the minimal overlapping BAC clones to genome sequencing and surveying the genetic resources and potential genetic markers, as well as comparing the similarity of coding and non-coding regions on genome. Now, Multinational Brassica Genome Project Consortium will start BAC end sequencing on 56,592 BAC clones of Brassica rapa.