Omics approaches and abiotic stress tolerance in legumes - Legumes Under Environmental Stress: Yield, Improvement and Adaptations - page 218

involved in responses against drought or salinity. The
cellular water deficit is the determining factor of a plant's
response to a particular environmental condition as it
triggers changes in the gene expression that define the
plant's response (Kosová et al., 2011). The induced or
repressed genes impact many plant processes like metab-
olism, signalling, transport, transcription, etc. The genes
that respond to abiotic stress can be classified according
to the time they take to be expressed once the plant has
been exposed to the abiotic stress: some are expressed
immediately in a matter of seconds to minutes while
others take longer to respond, from hours to days or
even weeks (Ramanjulu & Bartels, 2002). The early
response genes could be taken as genes responsible for
initial protection and the regulation of other genes
involved, including the genes encoding protein kinases
and transcription factors (Opdenakker et al., 2012). The
genes that respond to stress, on the other hand, may
play a role in facilitating the plant's adaptation to
the stress, such as the genes encoding proteins like
heat-shock proteins, ROS scavenger proteins, etc.
(Ramanjulu & Bartels, 2002).
Several methods can potentially be used for the pro-
filing of gene expression, including a variety of microarrays,
macroarrays and differential display, which could then be
validated by real-time quantitative polymerase chain
reaction (qPCR) (Butte, 2002). Transcriptomic analysis
can be used to screen for candidate genes that play a role
in the legume's response, which can then be used in
legume improvement (Garg et al., 2011; Jogaiah et al.,
2012). Determination of large-scale transcriptome profiles
can be carried out with methods like serial analysis of
gene expression (SAGE), DNA microarrays or the fairly
recent technique of digital gene expression (DGE), which
employs next generation sequencing (NGS)-based tools
like RNA-sequencing (RNA-seq) (Cramer et al., 2011).
The NGS approach allows the cell transcripts to be deci-
phered at the sequence level. This has the potential to
revolutionize research on legumes, which are now under-
going sequencing of their genomes. The aforementioned
approach can tackle the problems presented by the
massive genomes of legumes; moreover, NGS has also
circumvented issues like compromised sequence accu-
racy due to short sequence lengths, sequencing errors
characteristic of the methods used, and also the absence of
physical clones. NGS-based methods can prove to be
cost-efficient platforms that can be used to predict the
responses of legumes under certain abiotic stress

conditions, thus allowing assessment of the legume's
genome even at the functional level (Ohtsu et al., 2007).

13.3.1 Chickpea
Chickpea ( Cicer arietinum) is globally ranked third of the
commercially important legume crops. Drought is a
major abiotic stress affecting the yield of this legume
(Jukanti et al., 2012; Thudi, 2013a,b). Molina et al.
(2008) used SuperSAGE (a modified version of SAGE)
to analyse the response of chickpea roots to drought.
In order to do so, 8,023,826 base pair tags were
sequenced. These tags represented 17,493 unique tran-
scripts (UniTags) from roots exposed to drought and
those kept under control conditions. A total of 43% of
the UniTags (7532 in number) were more than 2.7-fold
differentially expressed, and the regulation of 5.0%
(880) of tags increased eight-fold when exposed to
stress. The large size of the tags made possible the
unambiguous annotation of 22% (3858) UniTags when
entered into public databases. This study comprehen-
sively showed that multiple processes including signal
transduction, transcriptional regulation, accumulation
of osmolytes and also ROS scavenging experience
extensive transcriptional remodelling in the roots as an
early response to stress imposed by drought conditions,
hence suggesting potential targets for improvement of
drought tolerance in chickpea through breeding.
Another study (De Domenico et al., 2012) aimed to
analyse the effect of the phyto-oxylipin pathway on
the chickpea response to drought conditions. In this
comparative study, the key genes involved were assessed
for their expression through analysis by qPCR using
commercially available TaqMan assays. Samples were
taken from the roots of stressed and non-stressed,
drought-sensitive and drought-tolerant chickpea. It was
concluded that the drought-tolerant chickpea reacted
to the stress with an earlier and sustained activation of
the following genes: Mt- LOX 1, Mt- HPL 1, Mt- HPL 2,
Mt- AOS and Mt- OPR . It was also shown that the overex-
pression of these genes was positively correlated with
levels of the major oxylipin metabolites from the AOS
branch of the phyto-oxylipin pathway, ultimately
leading to jasmonate synthesis. Higher levels of jas-
monic acid (JA), its precursor 12-oxophytodienoic acid
and JA-isoleucine were specifically found in the root
tissue of the chickpea variety that showed tolerance,
hence leading to the assumption that jasmonates play a
vital role in the early signalling response of the legume