Genomic Distribution of Simple Sequence Repeats in Brassica rapa

  • Hong, Chang Pyo (Department of Horticulture, College of Agriculture and Life Science, Chungnam National University) ;
  • Piao, Zhong Yun (College of Horticulture, Shenyang Agricultural University) ;
  • Kang, Tae Wook (Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Batley, Jacqueline (Primary Industries Research Victoria, Department of Primary Industries, Victorian AgriBioscience Centre) ;
  • Yang, Tae-Jin (Department of Plant Science, College of Agriculture and Life Sciences, Seoul National University) ;
  • Hur, Yoon-Kang (Department of Bioscience, School of Bioscience and Biotechnology, Chungnam National University) ;
  • Bhak, Jong (Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Park, Beom-Seok (Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration) ;
  • Edwards, David (Primary Industries Research Victoria, Department of Primary Industries, Victorian AgriBioscience Centre) ;
  • Lim, Yong Pyo (Department of Horticulture, College of Agriculture and Life Science, Chungnam National University)
  • Received : 2006.12.28
  • Accepted : 2007.03.06
  • Published : 2007.06.30

Abstract

Simple Sequence Repeats (SSRs) represent short tandem duplications found within all eukaryotic organisms. To examine the distribution of SSRs in the genome of Brassica rapa ssp. pekinensis, SSRs from different genomic regions representing 17.7 Mb of genomic sequence were surveyed. SSRs appear more abundant in non-coding regions (86.6%) than in coding regions (13.4%). Comparison of SSR densities in different genomic regions demonstrated that SSR density was greatest within the 5'-flanking regions of the predicted genes. The proportion of different repeat motifs varied between genomic regions, with trinucleotide SSRs more prevalent in predicted coding regions, reflecting the codon structure in these regions. SSRs were also preferentially associated with gene-rich regions, with peri-centromeric heterochromatin SSRs mostly associated with retrotransposons. These results indicate that the distribution of SSRs in the genome is non-random. Comparison of SSR abundance between B. rapa and the closely related species Arabidopsis thaliana suggests a greater abundance of SSRs in B. rapa, which may be due to the proposed genome triplication. Our results provide a comprehensive view of SSR genomic distribution and evolution in Brassica for comparison with the sequenced genomes of A. thaliana and Oryza sativa.

Keywords

Arabidopsis thaliana;Brassica rapa ssp. pekinensis;Genomic Distribution;Microsatellite;Simple Sequence Repeat (SSR)

Acknowledgement

Supported by : Korean Science and Engineering Foundation

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