Real-time PCR: what relevance to plant studies?

Gachon, Claire M. M.; Mingam, Annaïck; Charrier, Bénédicte

doi:10.1093/jxb/erh181

Cited by 390 publications

(275 citation statements)

References 92 publications

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“…MIPs can be classified into 4 subfamilies including plasma membrane intrinsic protein (PIP), tonoplast intrinsic protein (TIP), NOD26-like intrinsic protein (NIP) and small basic intrinsic protein (SIP). The recently developed technique of real-time RT-PCR using TaqMan-minor grove binder (MGB) probe, which has high specificity and sensitivity [25], provides a powerful tool for quantitatively investigating the overall expression of gene families with many members sharing high homology, such as the plant MIP family.…”

Section: Introductionmentioning

confidence: 99%

Water relations and an expression analysis of plasma membrane intrinsic proteins in sensitive and tolerant rice during chilling and recovery

et al. 2006

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A symptom of chilling injury is development of water deficit in shoots, resulting from an imbalance of water transport and transpiration. In this work, two rice varieties (Oryza sativa L. var. Wasetoitsu and Somewake) seedlings were chilled at 7 o C, followed by recovery at 28 o C. Based on the growth phenotype and electrolyte leakage tests, Somewake was shown to be a chilling-tolerant variety, and Wasetoitsu a chilling-sensitive one. The chilling stress reduced markedly the relative water content (RWC) of leaves, accumulative transpiration and osmotic root hydraulic conductivity (Lp) in both varieties. But when returned to 28 o C, the water relation balance of Somewake recovered better. The mRNA expression profile of all the 11 plasma membrane intrinsic proteins (PIPs), a subgroup of aquaporins, was subsequently determined by real-time reverse transcription (RT)-PCR with TaqMan-minor grove binder (MGB) probes derived from rice var. Nipponbare during chilling treatment and recovery. Most of the PIP genes was down-regulated at the low temperature, and recovered at the warm temperature. The relative expression of some PIPs in both Somewake and Wasetoitsu decreased in parallel during the chilling. However during the recovery, the relative expression of OsPIP1;1, OsPIP2;1, OsPIP2;7 in shoots and OsPIP1;1, OsPIP2;1 in roots were significantly higher in Somewake than Wasetoitsu. This supports the role of PIPs in re-establishing water balance after chilling conditions. We discuss the diversified roles played by members of the aquaporin PIP subfamily in plant chilling tolerance depending on aquaporin isoforms, plant tissue and the stage of chilling duration.

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Section: Introductionmentioning

confidence: 99%

Water relations and an expression analysis of plasma membrane intrinsic proteins in sensitive and tolerant rice during chilling and recovery

et al. 2006

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“…This is especially the case for quantitative reverse transcription (qRT)-PCR studies, which are growing in importance as a means to validate data from whole-genome oligonucleotide arrays and as a primary source of expression data for smaller sets of genes Gachon et al, 2004). Some of the best known and most frequently used reference transcripts for qRT-PCR in plants and animals include those of 18S rRNA, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor-1a (EF-1a), polyubiquitin (UBQ), actin (ACT), and a-tubulin and b-tubulin (TUA and TUB, respectively) genes (Goidin et al, 2001;Bustin, 2002;Kim et al, 2003;Andersen et al, 2004;Brunner et al, 2004;Dheda et al, 2004;Radonić et al, 2004).…”

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confidence: 99%

Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis

et al. 2005

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Gene transcripts with invariant abundance during development and in the face of environmental stimuli are essential reference points for accurate gene expression analyses, such as RNA gel-blot analysis or quantitative reverse transcription-polymerase chain reaction (PCR). An exceptionally large set of data from Affymetrix ATH1 whole-genome GeneChip studies provided the means to identify a new generation of reference genes with very stable expression levels in the model plant species Arabidopsis (Arabidopsis thaliana). Hundreds of Arabidopsis genes were found that outperform traditional reference genes in terms of expression stability throughout development and under a range of environmental conditions. Most of these were expressed at much lower levels than traditional reference genes, making them very suitable for normalization of gene expression over a wide range of transcript levels. Specific and efficient primers were developed for 22 genes and tested on a diverse set of 20 cDNA samples. Quantitative reverse transcription-PCR confirmed superior expression stability and lower absolute expression levels for many of these genes, including genes encoding a protein phosphatase 2A subunit, a coatomer subunit, and an ubiquitin-conjugating enzyme. The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future.

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“…For small-and medium-scale expression profiling, quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) is also useful. Depending on the choice of primers and detection technologies used, qRT-PCR can profile a single gene or several hundreds of genes in a single experiment (Busch and Lohmann, 2007;Gachon et al, 2004). Because of recent advances in high-throughput sequencing-based methods, the current state-of-the-art in transcriptome analyses is RNA sequencing (RNA-Seq).…”

Section: Gene Discoverymentioning

confidence: 99%

The Potential of Transcription Factor-Based Genetic Engineering in Improving Crop Tolerance to Drought

Rabara¹,

Tripathi

Rushton³

2014

OMICS: A Journal of Integrative Biology

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Drought is one of the major constraints in crop production and has an effect on a global scale. In order to improve crop production, it is necessary to understand how plants respond to stress. A good understanding of regulatory mechanisms involved in plant responses during drought will enable researchers to explore and manipulate key regulatory points in order to enhance stress tolerance in crops. Transcription factors (TFs) have played an important role in crop improvement from the dawn of agriculture. TFs are therefore good candidates for genetic engineering to improve crop tolerance to drought because of their role as master regulators of clusters of genes. Many families of TFs, such as CCAAT, homeodomain, bHLH, NAC, AP2/ERF, bZIP, and WRKY have members that may have the potential to be tools for improving crop tolerance to drought. In this review, the roles of TFs as tools to improve drought tolerance in crops are discussed. The review also focuses on current strategies in the use of TFs, with emphasis on several major TF families in improving drought tolerance of major crops. Finally, many promising transgenic lines that may have improved drought responses have been poorly characterized and consequently their usefulness in the field is uncertain. New advances in high-throughput phenotyping, both greenhouse and field based, should facilitate improved phenomics of transgenic lines. Systems biology approaches should then define the underlying changes that result in higher yields under water stress conditions. These new technologies should help show whether manipulating TFs can have effects on yield under field conditions.

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Real-time PCR: what relevance to plant studies?

Cited by 390 publications

References 92 publications

Water relations and an expression analysis of plasma membrane intrinsic proteins in sensitive and tolerant rice during chilling and recovery

Water relations and an expression analysis of plasma membrane intrinsic proteins in sensitive and tolerant rice during chilling and recovery

Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis

The Potential of Transcription Factor-Based Genetic Engineering in Improving Crop Tolerance to Drought

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