Planta

, Volume 229, Issue 1, pp 161–182

Identification of soybean microRNAs and their targets

Original Article

DOI: 10.1007/s00425-008-0818-x

Cite this article as:
Zhang, B., Pan, X. & Stellwag, E.J. Planta (2008) 229: 161. doi:10.1007/s00425-008-0818-x

Abstract

The microRNAs (miRNAs) are a newly identified class of small non-protein-coding regulatory RNA. Using comparative genomics, we identified 69 miRNAs belonging to 33 families in the domesticated soybean (Glycine max) as well as five miRNAs in the soybean wild species Glycine soja and Glycine clandestine. TaqMan® MicroRNA Assay analyses demonstrated that these miRNAs were differentially expressed in soybean tissues, with certain classes expressed preferentially in both a spatiotemporal and a tissue-specific manner. Detailed sequence analyses revealed that soybean pre-miRNAs vary in length from 44 to 259 nt with an average of 106 ± 45 nt, harbor mature miRNAs that differ in their physical location within the pre-miRNAs, and encode more than a single mature miRNA. Comparative sequence analyses of soybean miRNA sequences showed that uracil is the dominant base in the first position at the 5′ end of the mature miRNAs while cytosine is dominant at the 19th position, which is indicative that these two bases may have an important functional role in miRNA biogenesis and/or miRNA-mediated gene regulation. Soybeans were unique among plants in the frequency of occurrence of miRNA clusters. For the first time, antisense miRNAs were identified in plants. The five antisense miRNAs and their sense partners from soybean belonged to three miRNA families (miR-157, miR-162 and miR-396). Antisense miRNAs were also identified in soybean wild species. Mature antisense miRNA products appeared to have 1–3 nucleotide changes compared to their sense partners, which suggests that both strands of a miRNA gene can produce functional mature miRNAs and that antisense transcripts may differ functionally from their sense partners. Based on previously established in silico methods, we predicted 152 miRNA-targeted mRNAs, which included a large percentage of mRNAs that encode transcription factors that regulate plant growth and development as well as a lesser percentage of mRNAs that encode environmental signal transduction proteins and central metabolic processes.

Keywords

Antisense microRNAComparative genomicsExpressed sequence tagMicroRNA clusterPosttranscriptional gene regulationSoybean

Abbreviations

3′ UTR

3′ Untranslated region

AMFE

Adjusted MFE

ap2

Apetal 2

ARFs

Auxin response factors

CBF

CCAAT-binding transcription factor

EST

Expressed sequence tag

GSS

Genome survey sequence

GIF1

GRF1-interacting factor 1

HSP

Heat shock protein

miRNA

MicroRNA

MFEI

Minimal folding free energy index

pre-miRNAs

miRNA precusor

NCBI

National Center for Biotechnology Information

NAP

Nucleosome assembly protein

PCR

Polymerase chain reaction

qRT-PCR

Quantitative real time PCR

RISC

RNA-induced silencing complex

SBP

Squamosa-promoter binding protein-like protein

Supplementary material

425_2008_818_MOESM1_ESM.doc (121 kb)
MOESM1 Schematic representation of the miRNA gene search procedure for identifying soybeanhomologs based on established Arabidopsis miRNAs (DOC 121 kb)

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Baohong Zhang
    • 1
  • Xiaoping Pan
    • 2
  • Edmund J. Stellwag
    • 1
  1. 1.Department of BiologyEast Carolina UniversityGreenvilleUSA
  2. 2.Department of ChemistryWestern Illinois UniversityMacombUSA