Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview
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...
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| Format: | Article |
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MDPI AG
2016-05-01
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| Series: | Biology |
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| Online Access: | http://www.mdpi.com/2079-7737/5/2/20 |
| _version_ | 1797764437028896768 |
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| author | Khaled Moustafa Joanna M. Cross |
| author_facet | Khaled Moustafa Joanna M. Cross |
| author_sort | Khaled Moustafa |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-12T19:55:40Z |
| format | Article |
| id | doaj.art-2285c587f1b1474f96e8aad290862fa7 |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-12T19:55:40Z |
| publishDate | 2016-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-2285c587f1b1474f96e8aad290862fa72023-08-02T02:48:18ZengMDPI AGBiology2079-77372016-05-01522010.3390/biology5020020biology5020020Genetic Approaches to Study Plant Responses to Environmental Stresses: An OverviewKhaled Moustafa0Joanna M. Cross1Conservatoire National des Arts et Métiers, Paris 75003, FranceFaculty of Agriculture, Inonu University, Malatya 44000, TurkeyThe 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.http://www.mdpi.com/2079-7737/5/2/20plant stress toleranceenvironmental stressplant adaptationplant stress responsegene expression profilinggene expression studyDNA arraysmicroarraysnext generation sequencingNGS |
| spellingShingle | Khaled Moustafa Joanna M. Cross Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview Biology plant stress tolerance environmental stress plant adaptation plant stress response gene expression profiling gene expression study DNA arrays microarrays next generation sequencing NGS |
| title | Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview |
| title_full | Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview |
| title_fullStr | Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview |
| title_full_unstemmed | Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview |
| title_short | Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview |
| title_sort | genetic approaches to study plant responses to environmental stresses an overview |
| topic | plant stress tolerance environmental stress plant adaptation plant stress response gene expression profiling gene expression study DNA arrays microarrays next generation sequencing NGS |
| url | http://www.mdpi.com/2079-7737/5/2/20 |
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