Making the most of drought and salinity transcriptomics
More than 100 different studies of plant transcriptomic responses to salinity or drought-related stress have now been published. Most of these use microarrays or related high-throughput profiling technologies. This compels us to ask three questions in review: (1) what has transcriptomics contributed...
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Published in | Plant, cell and environment Vol. 33; no. 4; pp. 648 - 654 |
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Main Author | |
Format | Journal Article |
Language | English |
Published |
Oxford, UK
Oxford, UK : Blackwell Publishing Ltd
01.04.2010
Blackwell Publishing Ltd Blackwell |
Subjects | |
Online Access | Get full text |
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Summary: | More than 100 different studies of plant transcriptomic responses to salinity or drought-related stress have now been published. Most of these use microarrays or related high-throughput profiling technologies. This compels us to ask three questions in review: (1) what has transcriptomics contributed to our understanding of stress physiology; (2) what limits the ability of transcriptomics to contribute to increases in stress tolerance; and (3) given these limits, what are the most appropriate uses of transcriptomics? We conclude that although microarrays are now a mature technology that accurately describes the transcriptome, the consistently low correlation between transcript abundance and other measures of gene expression imposes an inherent limitation that cannot be ignored. Further limitations on the relevance of transcriptomics arise in some cases from experimental practices related to the treatment regimen and the selection of tissue or germplasm. Nevertheless, there is good evidence to support the continued use of transcriptomics, especially emerging techniques such as RNA-Seq, as a screening tool for candidate gene discovery. Microarrays can also be valuable in analysing the transcriptome per se (e.g. when describing the phenotype of a transcription factor mutant or discovering non-coding RNA species), and when integrated with other types of data including metabolomic analyses. |
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Bibliography: | http://dx.doi.org/10.1111/j.1365-3040.2009.02092.x ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-3 content type line 23 ObjectType-Review-1 |
ISSN: | 0140-7791 1365-3040 |
DOI: | 10.1111/j.1365-3040.2009.02092.x |