3. Map-based cloning of abiotic stress-related genes

Exploring genome sequences of Arabidopsis and rice and progress toward development of molecular markers and some new techniques has enabled positional cloning of mutated genes and natural alleles. A large number of molecular markers including single nucleotide polymorphisms (SNPs), simple sequence repeats (SSRs) and insertions/deletions (InDels) are available for Arabidopsis and rice plants. Map-based cloning approach that uses these various molecular markers have been used to identify a large number of abiotic stress-related genes such as the salt overly sensitive (SOS1, SOS2, SOS3, SOS4 and SOS5) genes, and other stressresponsive genes [10]. For generation of mutant lines, ethyl methane sulfonate and irradiations have been extensively used so far. In addition, the recent development of new techniques such as stress-associated genes (SAGs) and TILLING have added new dimensions in identifying mutations in stress-related genes and variant alleles [12]. In the near future, these techniques will be available for a number of crop plants such as Arabidopsis, wheat, maize, rice and brassica [13].

low number of Arabidopsis and rice tagged genes that code for clear phenotypes [28]. Recently, traps and activation tagging have been focused as the alternative means of gene tagging [29, 30]. Trap and activation techniques have been widely used for generation of tagged popu-

Understanding Plant Responses to Drought and Salt Stresses: Advances and Challenges in "Omics" Approaches

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Progress in transcriptomic analysis tools has revealed massive genomic sequence information in many plants. Identification of the partial or complete cDNAs sequences provide a holistic picture of the transcriptomes. The available ESTs are organized in three main databases, that is, NCBI, TIGR and Sputnik, which organize these ESTs with fully characterized gene sequences. Abiotic stress-related ESTs have contributed a great deal in exploring gene expression profiles

In recent years, different functional and molecular tools were used to identify abiotic stressresponsive genes in plants. These included genome wide physical and genetic mapping of chromosomes, isolation and sequencing of genes, ESTs, proteomics techniques and cDNA microarray analysis [32]. Particularly, the cDNA and microarrays were widely used to study gene expression profiles in Arabidopsis, potato, rice, sorghum, maize and wheat under abiotic stresses. The identified genes/proteins include late embryogenesis abundance (LEA) proteins,

The genomic approaches related to abiotic stress tolerance in plants are summarized (Table 1). In one study, Oono et al. [33] used a full-length cDNA microarray containing 7000 Arabidopsis full-length cDNAs and identified 152 rehydration-inducible genes. Among the 152 rehydration-inducible genes, 58 genes showed proline- and hypoosmolarity-inducible gene expression. Similar study was conducted in Arabidopsis under drought stress [34]. Transcriptomic analysis of M. sativa and M. esculenta revealed expression of several genes responsive to salt and drought, respectively [35, 36]. In rice plants, the pioneering work came from Rabbani et al. [37]. They used cDNA and gel microarray analysis to identify cold, drought, salinity and ABA inducible genes. They identified 73 stress inducible genes, among which 15 genes were highly responsive to all four treatments. Lan et al. [38] determined and compared the drought and wounding stress-related gene expression profiles. Drought stress regulated many of the pollination/fertilization-related genes. Similarly, the drought stress-related transcriptomic analysis was conducted in some other studies in rice [39]. Using a cDNA microarray, 486 salt responsive ESTs were determined in shoots of rice plants under salt stress [40]. Moreover, Hmida-Sayari et al. [41] used the cDNA amplified fragment length polymorphism (AFLP) technique to investigate the expression profile of potato under salt stress. The expression profile showed 5000 bands, of which 154 were up-regulated, while 120 were down-regulated. Most of these ESTs were found to have a role in biotic and abiotic stresses. Sequence comparison of some of these fragments revealed close homologies with proteins, involved in cell wall structure, stress proteins such as glyceraldehyde dehydrogenase and proteins related to hypersensitive response to pathogens. Approximately 20,000 ESTs were generated from a cDNA library constructed

compatible osmolytes, ROS scavengers and proteins involved in signal transduction.

lations of Arabidopsis and rice.

5. Transcriptomic analysis

of stress tolerance-related traits in in Arabidopsis and rice [31].

Map-based cloning strategy has also been exploited to unravel abiotic stress-related QTLs in plants. As abiotic stress tolerance trait is polygenic in nature, the QTLs studies have received immense importance in understanding stress responses [14]. Recently, using map-based cloning, a large number of drought and salt stress-related QTLs have been reported in crop plants. QTLs were mapped in Oryza sativa for abiotic stress tolerance [15, 16], Brassica napus for salt tolerance [17], maize for salt tolerance [18], wheat for drought tolerance [19] and cotton for salt tolerance [20]. Gene stacking approach through marker-assisted selection was successfully used in an elite rice cultivar for stacked QTLs related to biotic and abiotic stresses (submergence and salinity tolerance) [21, 22]. Two out of 10 pyramid lines showed adequate tolerance to all tested stresses including abiotic stresses. Similar studies using abiotic stress tolerance genes/QTLs need to be extended to other crop plants.
