Physiology and Molecular Biology of Stress ... - KHAM PHA MOI

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A.K. Tyagi, S. Vij and N. Saini
(Martienssen, 1998). This is because insertional mutagenesis not only causes a mutation
but also tags that region and helps in its identification. The advantage of insertional
mutagenesis is enhanced by the large collection of these mutants and their
sequenced insertion sites available in public databases. Transgenics are commonly
used for insertional mutagenesis. Analysis of function of a gene in one organism can
lead to identify function of its orthologues in other organisms. These results however,
can not be taken as absolute but only as preliminary clues for identifying gene function.
For instance, the Arabidopsis LEAFY (LFY) controls the formation of floral meristems
whereas the LFY homologue in rice, RFL, is involved in panicle branch initiation (Jeon
and An, 2001).
One area of interest for functional genomics of plants is stress tolerance.
Stresses reduce plant productivity, especially it has been reported that abiotic stresses
account for the maximum loss of plant productivity compared to any other factor
(Cushman et al., 1999). Efforts of plant scientists worldwide are to successfully bring
their research to practical use in the field. The endeavor will be successful only when
the understanding of the complexity of stress signaling and plant adaptive processes is
complete. This would require analysis of the function of numerous genes involved in
stress response by way of genomics approaches that would help assign function to
each gene.
2. EXPRESSION GENOMICS
Gene expression is highly influenced and is up- or down-regulated by the environment.
The expression of a gene or a group of genes during a specific stage reflects on functional
relevance. Various methods are available for detecting and quantification of gene
expression including northern blotting (Alwine et al., 1977), S1 nuclease protection
(Berk and Sharp, 1977), EST library (Adams et al., 1991), differential display and its
modifications (Liang and Pardee, 1992), Serial Analysis of Gene Expression or SAGE
(Velculescu et al., 1995) and microarray (Duggan et al., 1999). Some of these providing
information about dynamic state of expression, representing the whole genome, are
discussed here.
2.1. ESTs and cDNA Library
Demarcation of a gene in eukaryotes is more difficult as compared to prokaryotes
because their genes contain introns. Complementary DNAs (cDNAs) help in discovery
of new genes, polymorphism and gene expression (Ewing et al., 1999; Mekhedov et al.,
2000; Shannon et al., 2003; Zhu et al., 2003). The mRNAs which are found more abundant
in tolerant genotypes or tissues under stress conditions might be expected to play
an important role in stress tolerance and creating a cDNA library from these genotypes/
tissues would help in discovery of such genes and understanding their role in tolerance
mechanisms.