Plant & Animal Genomes XIX Conference

January 15-19, 2011
Town & Country Convention Center
San Diego, CA

Identification And Characterization Of Potential MicroRNAs And Their Targets In Brassica rapa L.

Vignesh Dhandapani , Nirala Ramchiary , Joonki Kim , Parameswari Paul , Yong Pyo Lim

  Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Gung-Dong, Yuseong- Gu Daejeon 305 764 Republic of Korea. Email: yplim@cnu.ac.kr Phone: +82 42 821 5739 Fax: +82 42 821 8847

MicroRNAs are recently discovered non coding small regulatory RNA molecules which negatively regulates gene expression. Although miRNAs have been identified and validated in many plant species, it is largely unknown in Brassica rapa (AA, 2n=20), an important Brassica crop with wide genetic and morphological diversity forming into several subspecies which are largely grown for vegetables, oilseeds and fodder crop production. In this study, using comparative genomics, we identified 186 miRNAs belonging to 55 families in B. rapa. The identified matured miRNA sequence length ranged from 18 to 22 nucleotides and pre-miRNAs sequence length ranged from 66 to 305 nucleotides, respectively. Comparison of four nucleotides revealed that “Uracil” is the dominant base in the first position of B. rapa miRNA suggesting important role of this nucleotide in miRNA-mediated gene regulation and in overall “Adenine” and “Guanine” nucleotides were dominant both in matured and pre-miRNA sequences, respectively. One DNA sequence was identified producing both sense and antisense identical matured miRNAs belonging to BrMiR 399 family. In silico analyses using previously established methods could predict 66 miRNA-target mRNAs for 33 miRNA families. Majority of target genes were transcription factors that regulate plant growth and development followed by few target genes which are involved in fatty acid metabolism, glycolysis, biotic and abiotic stresses, and other cellular processes. Northern blot analyses of RNA samples prepared from 3 different B. rapa tissues for 8 miRNA families revealed that miRNAs are differentially expressed both quantitatively and qualitatively in different tissues of B. rapa.