Genomic Approaches

Plant adaptation to environmental stresses is controlled by a cascade of molecular networks. In this regard, the application of genomic technologies has made more impact on understanding the plant responses to the abiotic stresses (Cushman 2003). The technology has made remarkable success in understanding the abiotic stress tolerance at genome level with potential to modify plants' tolerance for increasing yield under stressful conditions (Bohnert et al. 2006). In contrast to traditional breeding and marker-assisted selection programs, the direct introduction of a small number of genes by genetic engineering has also become tangible and attractive as a rapid approach to improve the plants' stress tolerance (Cushman and Bohnert 2000; Popova et al. 2008) to re-establish homeo-stasis and to protect and repair damaged proteins and membranes (Wang et al. 2003).

In the course of studies on mechanism of abiotic stress tolerance, Arabidopsis thaliana has emerged as an excellent model system (Zhu 2001) because most of the crop plants are glycophytes. However, study of some novel mechanisms unique to halophytes or stress-tolerant plants may be difficult with Arabidopsis and this has been made possible by the available genome information on Mesembryanthemum crystallinum, which, when compared with the Arabidopsis genome, seems to contain a number of transcripts that have no counterparts (Wang et al. 2004b). Thereafter, several halophytes such as M. crystallinum, Suaeda species, Atriplex species have been employed to dissect out the molecular basis of stress tolerance mechanism of the halophytes. Recently, Thellungiella halophila (salt cress), a member of the Brassicaceae, has emerged as a

Fig. 2.2 The salinity stress responses (growth, redox, and energy status) of Sesuvium portulacastrum exposed to optimum (250 mM) and supra-optimal (1,000 mM) concentrations of NaCl

model for understanding adaptation of the halophytes to abiotic stress tolerance due to its homology with the glycophyte model, A. thaliana (Wang et al. 2004b; Amtmann 2009). This halo-phyte has the ability to grow in high salt concentrations which otherwise become inhibitory for the growth of its salt-sensitive relative A. thaliana and other crop plants (Zhu 2001; Nah et al. 2009). The salient features of T. halophila such as small diploid genome (240 Mb and 2n = 14), short and self-fertile life cycle and ease of floral dipping method of transformation have enabled it as a successful candidate for molecular detailing of its response to abiotic stress tolerance and relative comparison with A. thaliana. The comparative genomics of T. halophila and A. thaliana revealed extensive and novel information on presence of differential genes responsible for abiotic stress tolerance in T. halophila in comparison to A. thaliana (Nah et al. 2009). Taji et al. (2004) studied the differences in the regulation of salt tolerance between salt cress and Arabidopsis by analyzing the gene expression profiles using a full-length Arabidopsis cDNA microarray. Only a few genes were induced by 250 mM NaCl in salt cress stress compared to Arabidopsis. Even in the absence of stress, a large number of known abiotic- and biotic-stress inducible genes, including Fe-SOD, P5CS, PDF1.2, AtNCED, P-protein, b-glucosidase, and SOS1, were expressed at high levels. The study also found salt cress to be more tolerant to oxidative stress than Arabidopsis. The salt tolerance mechanisms between salt-sensitive glyco-phytes and salt-tolerant halophytes could result from alterations in the regulation of the same basic set of genes involved in salt tolerance among these plants. Kant et al. (2006) used gene-specific primers of Arabidopsis that showed similar realtime PCR amplification efficiencies with both A. thaliana and T. halophila cDNA and concluded that the expression of specific salt tolerance orthologues differs between unstressed and stressed plants of both species.

The development of expressed sequence tags (ESTs) and cDNA libraries using various genomic approaches such as suppressive subtractive hybridization (SSH), differential display reverse transcription-polymerase chain reaction (DDRT-PCR), representational difference analysis (RDA), serial analysis of gene expression (SAGE), and cDNA microarray (Breyne and Zabeau 2001) provided an enormous databases for understanding the genetic network involved in abiotic stress tolerance mechanism of halophytes (Wang et al. 2004b; Kore-eda et al. 2004; Popova et al. 2008). Using this approach, various genes responsible for stress tolerance have been isolated from halo-phytes and cloned or overexpressed in the bacterial systems as well as sensitive cultivars of glycophytes to enhance the stress tolerance capacity and improve crop yield (Table 2.3).

Transcript-profiling experiments in Arabi-dopsis in response to drought, cold, or salinity stresses using the Arabidopsis GeneChip array or full-length cDNA microarrays have shown that extensive changes occur in the transcriptome of Arabidopsis (Fowler et al. 1999; Kreps et al. 2002; Seki et al. 2002). It is known that approximately 30% of the transcriptome on the Arabidopsis GeneChip 8 K oligoarray changed in stress treatments (Kreps et al. 2002) . The expressed sequence tag analyses of Thellungiella clones revealed 90-95% identities between Thellungiella and Arabidopsis cDNA sequences (Wang et al. 2004a, b; Wong et al. 2006). In a comparison of three stresses (cold, low water availability, and saline conditions) as well as recovery from water deficits in Thellungiella, Wang et al. (2006) employed an expression profiling strategy to identify stress responses. There was not much degree of overlap among genes responsive to drought, cold, or salinity suggesting relatively few common end responses triggered by these stresses existed in this halophyte. While Thellungiella had shown activation of the expression of some well-known stress-responsive genes, it was found to downregulate a large number of biotic stress-related genes under drought and salinity treatments. The study has made a significant step in showing the emergence of Thellungiella as a model species for the molecular elucidation of abiotic stress tolerance, and that Thellungiella responds precisely to environmental stresses, thereby conserving energy and resources and maximizing its survival potential.

SOS1 (Salt Overly Sensitive 1) is known to play key role in the ion homeostasis mechanism movement (Shi et al. 2000) . Although SOS1 has been intensely studied in Arabidopsis, its involvement in the salt tolerance of halophytes is not much known. Oh et al. (2009) investigated the role(s) by which ThSOS1, the SOS1 homolog in Thellungiella, was involved in modulating the halophytic character using ectopic expression of the gene in yeast and in Arabidopsis and Thellungiella SOS1-RNA interference (RNAi) lines. The knockdown of SOS1 expression totally altered Thellungiella into a salt-sensitive plant like Arabidopsis. The authors found that the activity of ThSOS1 could limit Na+ accumulation and the distribution of Na+ ions.

Table 2.3 Source of genes from halophytes for the improvement of abiotic stress tolerance

Source organism


Trait improved

Target organism


Atriplex gmelini

Vacuolar Na+/K+ antiporters AgNHXl

Eightfold higher activity of the vacuolar-type Na+/H+ antiporter

Otyza sativa

Ohta et al. (2002)

Medicago sativa

Vacuolar Na+/K+ antiporters MsNHXl

Increased osmotic adjustment and MDA content

A. thaliana

Bao-Yan et al. (2002)

Aeluropus littomlis

Vacuolar Na+/K+ antiporters AINHX1

Compartmentalize more Na+ in roots and keep a relative high K+/Na+ ratio in the leaves

N. tabacum

Zhang et al. (2008)

Atriplex centralasiatica

Betaine aldehyde dehydrogenase AcBADH

Improved synthesis of glycine betaine

N. tabacum

Yin et al. (2002)

Suaeda liaotungensis. Beta vulgaris, Atriplex hortensis, A. nummularia

Choline monooxygenase CMO

Three- to sixfold increased activity of CMO increases glycine betaine synthesis

N. tabacum

Russell etal. (1998). Shen et al. (2001). Tabuchi et al. (2005). and Li et al. (2003. 2007)

Avicennia marina

Monodehydroascorbate reductase (MDHAR)

Ascorbate regeneration and ROS scavenging

N. tabacum

Kavitha et al. (2010)

Sesuvium portulacastrum

Fructose-1,6-bisphosphate aldolase SpFBA

Strongly expressed in roots than in leaves and stems under abiotic stresses

Escherichia coli

Fan et al. (2009)

Mesembryanthemum crystallinum

IMT1, myo-Inositol O-methyl-transferase

Inositol methylation

E. coli

Rammesmayer et al. (1995)

Thellungiella halophila

FLC gene

Controls vernalization response pathway

T. halophila

Fang et al. (2006)

Suaeda salsa

Peroxiredoxin Q gene SsPix Q

Thioredoxin-dependent peroxidase activity

E. coli

Guo et al. (2004)

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