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transcriptome level using DeepSuperSAGE. From a total
of 144,200 analysed 26 bp tags in roots and nodules
together, 21,401 unique transcripts were identified. Of
these, only 363 and 106 specific transcripts, respectively,
were commonly upregulated or downregulated (>3.0-
fold) under salt stress in both organs, evidencing a
differential organ-specific response to stress. It was
found that transcripts were associated with the genera-
tion and scavenging of reactive oxygen species (ROS), as
well as being involved in Na + homeostasis. Although
both processes are already very well characterized in
other plants, the information generated in this study is
very valuable. Additionally, a set of more than 15 candi-
date transcripts were proposed to be potential components
of the salt overly sensitive (SOS) pathway in chickpea.
Newly identified transcript isoforms are potential targets
for breeding novel cultivars with high salinity tolerance.
This study proves that these targets can be combined
into breeding schemes by using microarrays and RT-PCR
assays downstream of the generation of 26 bp tags by
SuperSAGE (Molina et al., 2011).
A study was conducted to isolate and characterize a
novel JAZ family gene, GsJAZ2 , from G. soja following
exposure to salt, alkali, cold and drought. Subcellular
localization studies using a green fluorescent protein
(GFP) fusion protein showed that GsJAZ2 was local-
ized to the nucleus. These results suggest that the
newly isolated wild soybean GsJAZ2 is a positive regu-
lator of plant salt stress tolerance (Zhu et al., 2012). A
study by Song et al. (2012) described the identification
by microarray analysis of 49 soybean transcription
factors thought to be inducible by salinity stress. A
semi-quantitative RT-PCR-based expression assay con-
firmed the salinity stress inducibility of 45 of these 49
transcription factors. Salinity stress was revealed to
affect the methylation status of four of these ten tran-
scription factors (one MYB, one b-ZIP and two AP2/
DREB family members). Chromatin immunoprecipita-
tion (ChIP) analysis indicated that the activation of
three of the four DNA methylated transcription factors
was correlated with an increased level of histone H3K4
trimethylation and H3K9 acetylation, and/or a reduced
level of H3K9 demethylation in various parts of the
promoter or coding regions. This study indicated a vital
role for gene activation/repression by DNA methyla-
tion and/or histone modification of some transcription
factor genes in soybean tolerance to salinity stress
(Song et al., 2012).
Another study was conducted to characterize the
biological functions of a receptor-like cytoplasmic
serine/threonine protein kinase gene, GsRLCK , which
was previously identified as a putative salt-alkali stress-
related gene from the transcriptome profiles of G. soja .
Bioinformatic analysis indicated that GsRLCK protein
comprises a conserved kinase catalytic domain and two
transmembrane domains at the N-terminus, but no typ-
ical extracellular domain. Consistently, GsRLCK-eGFP
fusion protein was observed on the plasma membrane,
but eGFP alone was distributing throughout the cyto-
plasm in onion epidermal cells. Quantitative real-time
PCR analysis revealed the induced expression of
GsRLCK by ABA, salt, alkali and drought stresses. The
study indicated that GsRLCK was a novel receptor-like
cytoplasmic protein kinase and played a crucial role in
plant responses to salt stress (Sun et al., 2013).
The transcriptional profiles of genes in leaves and
roots of seedlings (two-leaf stage) of the soybean inbred
line HJ-1 were studied after 48 h under various stress
conditions including salt stress (120 mM NaCl) to iden-
tify responsible genes. Under salt stress, 874 genes were
upregulated in leaves, and 1822 genes were upregulated
in roots, compared with expression in the corresponding
organ in control plants. Furthermore, comparison of
gene expression among salt-, salt-alkali- and drought-
treated plants revealed that genes associated with
calcium signalling and nucleic acid pathways were
upregulated in the responses to all three stresses, indi-
cating a degree of cross-talk among these pathways.
This study provided new insights into the stress toler-
ance mechanisms of soybean (Fan et al., 2013).
The estimated size of the Glycine max genome is
1115 Mb in 20 chromosomes. A total of 950 Mb of the
genome sequence has been completed (Schmutz et  al.,
2010) giving a predicted 46,430 protein-coding genes
with high confidence, which is 70% more than
Arabidopsis thaliana . A total of 78% of the predicted
genes are present at the ends of chromosomes, and 75%
of the genes are present in multiple copies. A total of
12.2% of the predicted genes were identified as encod-
ing transcription factors.
Following transcript analyses, proteins are the sec-
ond most important aspect in defining an organism's
phenotype, representing the products of gene expres-
sion. To  encompass all the translational events from
mRNA  formation to functional proteins, analytical
platforms need to be able to evaluate not only the
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