PAG-XIII  Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA


P048 : Large Insert Libraries

Construction Of Bacterial Artificial Chromosome Libraries And Their Exploitation In Physical Mapping And Genome Characterization In Brassica rapa

Yong Pyo Lim1 , Jae Wook Bang2 , Yoon Kang Hur2 , Prikshit Plaha1, 3 , Beom-Seok Park4

1  Genome Research Center, and Department of Horticulture, Chungnam National University, Daejeon, 305-764, Korea
2  Genome Research Center, and Department of Biology, Chungnam National University, Daejeon, 305-764, Korea
3  Advanced Centre of Hill Bioresources and Biotechnology, HP Agricultural University, Palampur, 176 062, India
4  Brassica Genome Team, National Institute of Agricultural Biotechnology, RDA, Suweon, Korea

Bacterial artificial chromosome (BAC) system, commonly used for developing large insert libraries, is useful for genome research. By isolating high molecular weight leaf DNA of Chinese cabbage (Brassica rapa ssp. pekinensis) inbred line “Chiifu”, we constructed two BAC libraries using restriction enzymes, HindIII and BamHI. The HindIII library consists of 56,592 clones with an average insert size of 115 kb, whereas BamHI library has 50,688 clones with an average insert size of 124 kb. Together, these BAC libraries cover approximately 23 genome equivalents, considering the genome size of Chinese cabbage as 550 Mb. We constructed a physical map using HindIII library. The HindIII generated restriction fragments, resulting from 36,412 BAC clones, were called and normalized by IMAGE program and the contigs assembled using FPC program. The BAC clones could be assembled in 3,232 contigs, covering 407 Mb i.e. 74.0% of the genome.
From 6,849 BAC clones, we also generated 12,017 sequences of the HindIII library BAC clones with an average read length of 642 bp. Analysis using BLAST and motif searches revealed that 33.2%, 13.0%. 1.9% and 29.9% of the BAC-end sequences contained protein coding regions, transposable elements, microsatellites and tandemly satellite DNA, respectively. A comparison of the functional categories of protein-coding regions with those of Arabidopsis showed that proteins pertaining to metabolism, transcription and cell fate were comparatively higher in B. rapa. Sequence comparison in the two species indicated that genes of B. rapa showed duplications within the genome, and were homologous to those of Arabidopsis.