Molecular Techniques for Plants Gene Expression Analysis at the Transcriptomics Level

Environmental stresses such as drought, salinity, cold and heat stress as one of the consequences of climate change are the main factors of reduction in agricultural products. Study of gene expression (transcriptomic studies) plays an essential role in understanding the mechanism of plants in dealing with environmental stresses. Gene expression is the process by which information encoded in a gene is produced in the form of a transcript, which often the transcript itself or its protein product involves in various molecular processes and mechanisms in the cell and ultimately in the life of the organism. Assessing gene expression levels is an important step in elucidating gene functions temporally and spatially.

This review article is a content analysis study that has been performed by searching Transcriptome analysis, RNA sequencing, suppression subtractive hybridization, microarray, polymerase chain reaction keywords in related articles on google scholar, science direct, PubMed and scopus websites.

Decades ago, typical studies were focusing on a few genes individually via techniques such as northern blot, or RNA blot, western blot, microarray hybridization, subtractive hybridization (SH), suppression subtractive hybridization (SSH), real-time polymerase chain reaction (real-time PCR), whereas now researchers are able to examine whole genomes at once thanks to sequencing based approaches such as RNA sequencing (RNA-seq). The upgrade of throughput levels aided the introduction of systems biology approaches whereby cell functional networks can be scrutinized in their entireties to unravel potential functional interacting components. The birth of systems biology goes hand-in-hand with huge technological advancements and enables a fairly rapid detection of all transcripts in the studied biological samples. Even so, earlier technologies that were restricted to probing single genes or a subset of genes still have their place in the research laboratories.

The objective of this study was to describe the types of methods used in the gene expression analysis in plant responses to environmental stresses, or, more generally, any other conditions of interest. The choice of technique or strategy used is determined by the available technology and equipments along with the costs and limitations of the analysis. In selection of techniques for a particular study, these limitations should be minimized methodologically or statistically so that the results are reliable and representative of the situation under study.