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.
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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
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Acknowledgments
This work was partially supported by EU-FP6 Marie Curie International Reintegration Grant, Turkish National Academy of Sciences (TUBA-GEBIP) and Nebraska Turfgrass Association. Authors wish to acknowledge O. Cebeci, K. Yucebilgili and M. Aydin for the help with the preparing samples and data analysis.
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Communicated by R. Hagemann.
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Unver, T., Bakar, M., Shearman, R.C. et al. Genome-wide profiling and analysis of Festuca arundinacea miRNAs and transcriptomes in response to foliar glyphosate application. Mol Genet Genomics 283, 397–413 (2010). https://doi.org/10.1007/s00438-010-0526-7
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DOI: https://doi.org/10.1007/s00438-010-0526-7