title: Identification of potential microRNAs and their targets in Brassica rapa L.
abstract: MicroRNAs (miRNAs) are recently discovered, noncoding, small regulatory RNA molecules that negatively regulate gene expression. Although many miRNAs are identified and validated in many plant species, they remain largely unknown in Brassica rapa (AA 2n =, 20). B. rapa is an important Brassica crop with wide genetic and morphological diversity resulting in several subspecies that are largely grown for vegetables, oilseeds, and fodder crop production. In this study, we identified 186 miRNAs belonging to 55 families in B. rapa by using comparative genomics. The lengths of identified mature and pre-miRNAs ranged from 18 to 22 and 66 to 305 nucleotides, respectively. Comparison of 4 nucleotides revealed that uracil is the predominant base in the first position of B. rapa miRNA, suggesting that it plays an important role in miRNA-mediated gene regulation. Overall, adenine and guanine were predominant in mature miRNAs, while adenine and uracil were predominant in pre-miRNA sequences. One DNA sequence producing both sense and antisense mature miRNAs belonging to the BrMiR 399 family, which differs by 1 nucleotide at the, 20(th) position, was identified. In silico analyses, using previously established methods, predicted 66 miRNA target mRNAs for 33 miRNA families. The majority of the target genes were transcription factors that regulate plant growth and development, followed by a few target genes that are involved in fatty acid metabolism, glycolysis, biotic and abiotic stresses, and other cellular processes. Northern blot and qRT-PCR analyses of RNA samples prepared from different B. rapa tissues for 17 miRNA families revealed that miRNAs are differentially expressed both quantitatively and qualitatively in different tissues of B. rapa.
authors.affiliation: Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, 305-764, Korea.
authors.forename: Vignesh
authors.initials: V
authors.lastname: Dhandapani
authors.forename: Nirala
authors.initials: N
authors.lastname: Ramchiary
authors.forename: Parameswari
authors.initials: P
authors.lastname: Paul
authors.forename: Joonki
authors.initials: J
authors.lastname: Kim
authors.forename: Sun Hee
authors.initials: SH
authors.lastname: Choi
authors.forename: Jeongyeo
authors.initials: J
authors.lastname: Lee
authors.forename: Yoonkang
authors.initials: Y
authors.lastname: Hur
authors.forename: Yong Pyo
authors.initials: YP
authors.lastname: Lim
mesh_terms: D001483:Base Sequence; D015152:Blotting, Northern; D029741:Brassica rapa / Q000235:genetics / Q000378:metabolism; D035264:Flowers / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D035683:MicroRNAs / Q000032:analysis / Q000737:chemistry / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D012322:RNA Precursors / Q000032:analysis* / Q000737:chemistry; D018749:RNA, Plant / Q000032:analysis* / Q000737:chemistry; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014498:Uracil / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors; D018749:RNA, Plant; D014498:Uracil