Gene pyramiding and omics approaches for stress tolerance in leguminous plants - Legumes Under Environmental Stress: Yield, Improvement and Adaptations - page 269

anthracnose resistance ( Co-1 to Co-10 ) so that they can
be further used to pyramid a resistant cultivar through
MAS. Similarly, RAPD markers linked to the 11 genes
( Ur-1 to Ur-11 ) conferring rust resistance have been
used to integrate and pyramid rust resistance into
common bean cultivars. These markers have also been
used to combine rust resistance with resistance to other
diseases, such as bean common mosaic virus (BCMV),
bean golden mosaic virus (BGMV), common bacterial
blight and anthracnose (Stavely, 2000; Singh et al.,
2001). The genes Rsv1 , Rsv3 and Rsv4 were pyramided
for the trait soybean mosaic virus resistance in soybean
using a marker-assisted gene pyramiding approach
(Saghai Maroof et al., 2008; Shi et al., 2009).

stress QTLs in legumes is still at an early stage and
requires more study for its proper application to stressed
legumes.

16.2.2 Omics approaches
To address the drastic changes in plants under stress,
a comprehensive study that involves both quantitative
as well as qualitative analysis of genetic variation is
necessary at various molecular levels such as the
proteome, transcriptome and metabolome (Dita et al.,
2006). In recent years biotechnology has developed into
a significant tool to elucidate genetic variation in plants
under stress. Among the most important are the various
omics approaches, which have great potential for over-
coming stress in grain legumes and increasing their
tolerance to stress (Reddy et al., 2012). Omics approaches
include genomics, proteomics, transcriptomics, metabo-
lomics, functional genomics and genetic engineering.
These can provide insights into the physiological and
molecular changes in plants in response to variable
stress conditions, thereby informing the genetic basis of
stress adaptation.

16.2.1.6 Combined marker-assisted selection
To develop resistant cultivars to multiple stresses,
biotechnological techniques such as transgenesis or
mutagenesis and MAS can be combined to pyramid
multiple resistance genes (Dita et al., 2006). To increase
genetic gain, combined MAS may have advantages above
phenotypic screening or MAS alone (Lande & Thompson,
1990). Combined MAS may be used when additional
QTLs are unknown or when manipulation of a great
number of QTLs is required. This approach is more effi-
cient than phenotypic screening alone, particularly in
case of large population sizes and low trait heritability
(Hospital et al., 1997). MAS for improving insect resis-
tance in tropical maize was studied by Bohn et al. (2001).
They found that MAS alone was less efficient compared
to conventional phenotypic selection, while the efficiency
increased by using a combined MAS approach. One such
approach was also used in soybean to manage insect
resistance. This resulted in the development of resis-
tance to corn earworm ( Helicoverpa zea ) and soybean
looper ( Pseudoplusia includens ) in eight soybean lines
by combining two major insect-resistance QTLs and a
synthetic Bt gene ( cry1Ac ) (Walker et al., 2004).
Although there are considerable efforts to improve
the yield of pulses through conventional breeding
methods, the rate of progress is slow. This is because the
genotype of pulses is highly influenced by the environ-
mental factors that interact with the expression of
important quantitative traits (Kumar & Ali, 2006).
Therefore, this prompts the need for incorporating new
technologies in plant breeding programmes, such as
MAS and marker-assisted gene pyramiding or growing
of transgenic crops. But knowledge regarding abiotic

16.2.2.1 Transcriptomics
Transcriptomics allows one to screen the expression of
thousands of genes simultaneously. At any given time
and set of conditions, the total set of messenger RNAs
(mRNAs) in an organism is referred to as the transcrip-
tome and their analysis is termed transcriptomics. The
numerous plant genomic and transcriptomic studies of
plants under stress conditions that have been done in
recent years suggest that change in the plant system is
due to the interaction between the environmental and
internal conditions of the plant (Polesani et al., 2008).
Plants acclimatize to various abiotic and biotic stresses
by adopting complex, broad-spectrum molecular and
genetic mechanisms to counteract the effects of the
stresses. Many reports suggest that changes due to
stressed environment are induced at the transcriptional
level (Nakashima et al., 2009; Tran et al., 2010; Hadiarto &
Tran, 2011) (Figure 16.3).
Genome-wide sequencing (GWS) profiles the entire
DNA sequence of an organism's genome in one go using
oligo-probes to identify several stress-inducible genes
and transcriptomic studies using cDNA and oligonucle-
otide microarrays (Matsui et al., 2008, 2010). Another
important technique used for transcriptomic studies of
various legumes is quantitative real-time polymerase