Molecular Genetics and Genomics

, Volume 283, Issue 4, pp 397–413

Genome-wide profiling and analysis of Festuca arundinacea miRNAs and transcriptomes in response to foliar glyphosate application

  • Turgay Unver
  • Mine Bakar
  • Robert C. Shearman
  • Hikmet Budak
Original Paper

Abstract

Glyphosate is a broad spectrum herbicide which has been widely used for non-selective weed control in turfgrass management. Festuca arundinacea cv. Falcon was shown to be one of the tolerant turfgrass species in response to varying levels of glyphosate [5% (1.58 mM), 20% (6.32 mM)] recommended for weed control. However, there is a lack of knowledge on the mRNA expression patterns and miRNA, critical regulators of gene expression, in response to varying levels of glyphosate treatments. Here, we investigate the transcriptome and miRNA-guided post-transcriptional networks using plant miRNA microarray and Affymetrix GeneChip® Wheat Genome Array platforms. Transcriptome analysis revealed 93 up-regulated and 78 down-regulated genes, whereas a smaller number showed inverse differential expressions. miRNA chip analysis indicated a number of (34 out of the 853) plant miRNAs were differentially regulated in response to glyphosate treatments. Target transcripts of differentially regulated miRNAs were predicted and nine of them were quantified by quantitative real-time PCR (qRT-PCR). Target transcripts of miRNAs validate the expression level change of miRNAs detected by miRNA microarray analysis. Down-regulation of miRNAs upon 5 and 20% glyphosate applications led to the up-regulation of their target observed by qRT-PCR or vice versa. Quantification of F. arundinacea miRNA, homologous of osa-miR1436, revealed the agreement between the Affymetrix and miRNA microarray analyses. In addition to miRNA microarray experiment, 25 conserved F. arundinacea miRNAs were identified through homology-based approach and their secondary structures were predicted. The results presented serve as analyses of genome-wide expression profiling of miRNAs and target mRNAs in response to foliar glyphosate treatment in grass species.

Keywords

Festuca arundinecea Affymetrix GeneChip® Wheat Genome Array Glyphosate miRNA Transcriptome analyses 

Abbreviations

ΔG

Folding free energies

cDNA

Complementary DNA

DE

Differential expression

EPSPS

5-Enolpyruvylshikimate-3-phosphate synthase

EST

Expressed sequence tag

Far

Festuca arundinacea

ISH

Interspecies hybridization

MFE

Minimal folding free energy

miRNA

Micro-RNA

NAC5

NAC domain protein

ndhF

NADH dehydrogenase subunit F

NCBI

National Center of Biotechnology Information

nt

Nucleotide(s)

PEP

Glyphosate competes with phosphoenolpyruvate

Pre-miRNA

Micro-RNA precursor

Pri-miRNAs

Primary micro-RNAs

PCA

Principal component analysis

qRT-PCR

Quantitative real-time PCR

RMA

Robust multichip average

RT

Real time

RuBP

Ribulose bisphosphate

Ser

Serine

Thr

Threonine

Supplementary material

438_2010_526_MOESM1_ESM.xls (56 kb)
Supplementary material 1 (XLS 55 kb)
438_2010_526_MOESM2_ESM.xls (84 kb)
Supplementary material 2 (XLS 83 kb)
438_2010_526_MOESM3_ESM.doc (79 kb)
Supplementary material 3 (DOC 79 kb)
438_2010_526_MOESM4_ESM.doc (226 kb)
Supplementary material 4 (DOC 226 kb)

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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Turgay Unver
    • 1
  • Mine Bakar
    • 1
  • Robert C. Shearman
    • 2
  • Hikmet Budak
    • 1
  1. 1.Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural SciencesSabanci UniversityIstanbulTurkey
  2. 2.University of Nebraska-LincolnLincolnUSA

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