Abiotic Stress Responses in Plants: Unraveling the Complexity of Genes and Networks to Survive - Abiotic Stress: Plant Responses and Applications in Agriculture - page 72

Drought is the major constraint to increase yield in chickpea ( Cicer arietinum ) [288]. SuperS‐
AGE, an improved version of the serial analysis of gene expression (SAGE) technique, has been
employed in the analysis of gene expression in chickpea roots in response to drought [289]. To
achieve this goal 80,238 26 bp tags were sequenced representing 17,493 unique transcripts
(UniTags) from drought-stressed and non-stressed control roots. A total of 7,532 (43%) UniTags
were more than 2.7-fold differentially expressed, and 880 (5.0%) were regulated more than 8-
fold upon stress. Their large size enabled the unambiguous annotation of 3,858 (22%) UniTags
when searched against public databases. This comprehensive study demonstrated that signal
transduction, transcription regulation, osmolyte accumulation, and AOS scavenging undergo
a strong transcriptional remodeling in chickpea roots in early drought stress responses,
suggesting potential targets for breeding for drought tolerance.
High-throughput transcriptome sequencing and digital gene expression (DGE) profiling are
cost-efficient platforms that are predicted to change transcriptomic analysis, eliminating the
need for restriction enzyme digestion of DNA samples, PCR-based genomic amplification and
ligation of sequence tags; they are additionally a suitable choice for characterizing non-model
organisms without a reference genome [290-291]. Furthermore, RNA-seq can produce a
complete coverage of transcripts, providing information about the sequence, structure and
genomic origins of the entire transcript [285]. The dynamic transcriptome expression profiles
of poplar ( Populus simonii × Populus nigra ) under salt stress were investigated using Solexa/
Illumina digital gene expression technique [292]. A total of 5453, 2372, and 1770 genes were
shown to be differentially expressed after exposure to NaCl for 3 days, 6 days and 9 days,
respectively. Differential expression patterns throughout salt stress identified 572 genes, most
of them mapped to the Gene Ontology term “receptor activity”, “transporter activity” and
“response to stress”. Importantly this study showed that the greatest upregulation was
observed for the POPTR_0018s02240.1 transcript encoding a serine/threonine protein kinase.
Serine/threonine protein kinases have been reported to confer enhanced multi-stress tolerance
in many plants [293], suggesting that this gene can be a suitable target for biotechnological
manipulation with the aim of improving poplar salt tolerance.
The recent rapid accumulation of dataset containing large-scale gene expression profiles has
supported the development of dedicated web databases acting as large public repositories,
where data and underlying experimental conditions are widely described. A very complete
and comprehensive list of searching database may be found in [294]. With the completion of
the genome sequencing of several model and crop plants, these repositories can constitute
important functional resources to be explored to decipher the molecular mechanisms under‐
lying abiotic stress responses.
5.2. Proteomics
Proteomics may be defined as the science that studies the proteome, i.e. the number of proteins
expressed in a given cell, tissue, organ, organism or populations. Proteomics is normally
associated to two types of studies: 1) the characterization of a proteome in which all the proteins
expressed in a given cell, tissue, organ, organism or populations are identified; and 2) differ‐
ential proteomics in which a proteome of for instance a plant under control conditions is