Genetic approaches to study plant responses to environmental stresses

Abstract

Abstract:The assessment of gene expression levels is an important step toward elucidating gene functions temporally and spatially. Decades ago, typical studies were focusing on a few genes individually, whereas now researchers are able to examine whole genomes at once. 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 studied biological samples. Even so, earlier technologies that were restricted to probing single genes or a subset of genes still have their place in research laboratories. The objective here is to highlight key approaches used in gene expression analysis in plant responses to environmental stresses, or, more generally, any other condition of interest. Northern blots, RNase protection assays, and qPCR are described for their targeted detection of one or a few transcripts at a once. Differential display and serial analysis of gene expression represent non-targeted methods to evaluate expression changes of a significant number of gene transcripts. Finally, microarrays and RNA-seq (next-generation sequencing) contribute to the ultimate goal of identifying and quantifying all transcripts in a cell under conditions or stages of study. Recent examples of applications as well as principles, advantages, and drawbacks of each method are contrasted. We also suggest replacing the term "Next-Generation Sequencing (NGS)" with another less confusing synonym such as "RNA-seq", "high throughput sequencing", or "massively parallel sequencing" to avoid confusion with any future sequencing technologies.

Retracted Article: Investigation of yellow horn (Xanthoceras sorbifolia Bunge) transcriptome in response to different abiotic stresses: a comparative RNA-Seq study

“…15,16 The applications of NGS technologies are not only contributable to a deep investigation into the genomic resources for yellow horn, but also conducive to a quick identication of differentially expressed genes (DEGs), as well as the key metabolic pathways of yellow horn in response to abiotic stresses. 17,18 As one type of NGS, RNA-sequencing (RNA-Seq) can provide unprecedented opportunities for the generation of genomic information in uncharacterized earlier systems. 19,20 Recent literatures have also reported the transcriptome of many plants performed using RNA-Seq, such as tomato, 21 Rosa chinensis, 22 watermelon 23 as well as tobacco.…”

cDNA-AFLP ANALYSIS REVEALS DIFFERENTIAL GENE EXPRESSION IN RESPONSE TO SEED AGING IN SIBERIAN WILDRYE

“…Since there is no available database to gain genome sequences and very little is known about the genome structure. cDNA-AFLP technology is the best option for transcripts analysis because there is no requirement for sequence information and it enables to identify novel changed genes (Moustafa and Cross, 2016). cDNA-AFLP technology had been used to identify the differentially expression genes in seed aging of the other plants.…”