Identification and validation of conserved microRNAs along with their differential expression in roots of Vigna unguiculata grown under salt stress

  • Sujay Paul
  • Anirban Kundu
  • Amita PalEmail author
Original Paper


MicroRNAs (miRNAs) are 20–24 nucleotide long non-coding RNAs known to play important regulatory roles during plant development, organ morphogenesis, and stress responses by controlling gene expression. Although Vigna unguiculata (cowpea) is an economically important salt sensitive member of legumes, very little is known about the conserved miRNAs and their expression profile during salinity stress in this plant. In the present study using comparative genomic approach and following a set of strict filtering criteria we have identified 18 conserved V. unguiculata miRNAs belonging to 16 distinct miRNA families. Using these potential miRNA sequences 15 potential target genes were predicted and all of them were identified as transcription factors. Seven of these predicted V. unguiculata miRNAs were experimentally validated in the root tissues and found to be up-regulated during salt stress as revealed by quantitative real time PCR (qRT-PCR). Perfectly cleaved Auxin response factor (ARF), the target transcript of V. unguiculata miR160 was detected successfully by modified 5′ RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) method.


MicroRNA Salt stress Vigna unguiculata (cowpea) miRNA targets qRT-PCR 5′ modified RLM-RACE 



Expressed sequence tag


Genomic survey sequence


RNA induced silencing complex


Minimum folding free energy


Minimum folding free energy index


RNA ligase-mediated rapid amplification of cDNA ends


Quantitative real time PCR


Dana Farber Cancer Institute


Squamosa promoter binding protein


Squamosa promoter binding protein-like protein


Auxin response factor


Teosinte branched1-Cycloidea-Pcf


CCAAT-binding transcription factor


Nuclear factor Y






Tentative contigs


Small nuclear RNA



We are thankful to the Director, Bose Institute for providing the lab facilities; we also thank the Department of Biotechnology, India, for the financial assistance (Sanction no. BT/01/COE/06/03), a SRF to AK and a RA to SP.


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Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Division of Plant Biology, Bose InstituteKolkataIndia

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