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nodule metabolism in plants under abiotic stress have
been identified. Root nodular proteins (nif proteins) are
known to cleave ROS by making them susceptible to
proteolytic cleavage (Nakano et al., 2006). Proteomic
analysis of nodules can be achieved using techniques
such as 2D-SDS-PAGE (Siria et al., 2000; Lei et al., 2005;
Larrainzar et al., 2007; De-la-Pena et al., 2008). Formation
and breakdown of proteins in the nodules of  plants is
very important for growth, development, metabolism,
etc., making proteomic analysis of the nodules crucial
for an understanding of changes in protein-protein
interactions and protein profiling (Feller et al., 2008).
by studying two-variant crosses in soybean, i.e. S-100
(salt tolerant) × Tokyo (salt susceptible) was evaluated
using RFLP markers. An important QTL associated with
salt stress acclimatization was observed to be present
near the Sat_091 SSR marker on linkage group (LG) N
(Lee et al., 2004). Recent years have seen the
development of intervarietal molecular profiling with
the aid of SSRs, SNPs and gene-based molecular markers
in common bean, chickpea and soybean (Hwang et al.,
2009; Hanai et al., 2010; Nayak et al., 2010) (Table 16.2).
16.2.2.4 Functional genomics
Functional genomics is a field of modern biology that
aims at deciphering the functions of genes that are
sequenced. Numerous genome projects generated
extensive information about gene sequences of different
plant species, but decoding their functions becomes the
challenge that needs to be focused upon. Hence,
functional genomics, which uses methodologies of
reverse genetics, becomes important in recognizing the
associations between an organism's genome and its phe-
notype (Pevsner, 2009).
This technology gains more importance when applied
for the identification of genes that control stress toler-
ance or resistance in plants subjected to various biotic
and abiotic stresses, and it can be further used to develop
resistant varieties (Kudapa et al., 2013). Amongst the
leguminous plants, Medicago truncatula and Lotus
japonicus have been used as model plants to carry out
extensive molecular and genetic studies due to their
small genomes and simple genetic system (Handberg &
Stougaard, 1992; Cook, 1999).
The function of a gene can be identified by deactivat-
ing gene or by suppressing its expression. This can be
achieved by antisense RNA suppression, targeted gene
replacement, insertional mutagenesis, gene silencing
through RNAi and targeted induced local lesion in
genome (TILLING) approaches (Reddy et al., 2012). Of
these, RNAi-induced silencing - a post-transcriptional
gene silencing method - has been widely adopted. In
legumes, this technique has been successfully used in
Medicago , in which the importance of PIN proteins was
established by using RNAi. Reduction in PIN proteins
resulted in a reduced number of nodules thereby indi-
cating the role of these proteins in nodulation (Huo
et al., 2006). In soybean, RNAi was used to silence the
expression of the GmMIPS1 gene, which is responsible
for encoding myoinositol-1-phosphate, which further
16.2.2.3 Genomics
Genomics makes a vital contribution to understand
genetic diversity and underlies many modern approaches
to developing modified crops and gives new opportu-
nities for altering QTLs through marker-assisted selection.
Genomics approaches include a wide range of informa-
tive techniques such as development of molecular
markers, genome profiling, DNA sequencing, etc. (Reddy
et al., 2012). Certain genomics techniques such as
recombinant profiling, genome-wide association (GWA)
and QTL sequencing have provided immense amounts
of information and enabled a greater understanding of
the biochemical and molecular bases of genetic varia-
tion and signalling networks in numerous plant species
under abiotic interaction (Cross et al., 2006; Stitt et al.,
2010; Riedelsheimer et al., 2012).
Techniques being used for genomic analysis of plants
under environmental stresses include fluxomics, metab-
olomics, tissue-specific metabolite profiling and spatial
transcriptional changes (Gifford et al., 2008; Long et al.,
2010; Saito & Matsuda, 2010; Tohge et al., 2011; Bocobza
et al., 2012; Ferni & Morgan, 2013).
In recent years, development of next generation
sequencing (NGS) techniques has enabled the sequencing
of large genomes within a few hours and allows the
differential profiling of cell transcripts at the genomic
level. This technique has been useful even in the genomic
analysis of very large genomes including grain legumes
(Oldroyd, 2005; Thompson et al., 2005). Development of
linkage maps based on SSRs and genetic markers for pro-
filing and mapping of pathogen stress (i.e. ascophyta
blight disease)-responsive QTLs in food legumes has also
been done (Muehlbauer & Chen, 2007).
Several genetic alterations due to salt stress have been
reported in soybean. Various QTLs have been identified
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