Plant Cell, Tissue and Organ Culture (PCTOC)

, Volume 105, Issue 2, pp 233–242

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

Original Paper

Abstract

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.

Keywords

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

Abbreviations

EST

Expressed sequence tag

GSS

Genomic survey sequence

RISC

RNA induced silencing complex

MFE

Minimum folding free energy

MFEI

Minimum folding free energy index

RLM-RACE

RNA ligase-mediated rapid amplification of cDNA ends

qRT-PCR

Quantitative real time PCR

DFCI

Dana Farber Cancer Institute

SBP

Squamosa promoter binding protein

SPL

Squamosa promoter binding protein-like protein

ARF

Auxin response factor

TCP

Teosinte branched1-Cycloidea-Pcf

CBF

CCAAT-binding transcription factor

NFY

Nuclear factor Y

AP2

APETALA2

AGO1

Argonaute1

TC

Tentative contigs

snRNA

Small nuclear RNA

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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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