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

Freezing Stress
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genes at the transcriptional level (Schena et al., 1995). Genomic sequencing projects
have provided genetic information for entire genomes , however, the expression or
function of many of these genes during a physiological process has yet to be determined.
The ability to quantify and compare gene expression on a global scale is a
powerful analytic tool. Microarray analysis makes it possible to potentially monitor
and quantitate transcript levels of an entire genome in any biological state (eg. Response
to pathogens, abiotic stress, developmental stage, etc.) (Brown and Botstein
1999; Duggan et al 1999). The information obtained from this approach can be used to
elucidate biochemical and regulatory pathways. Candidate genes can be selected based
on environmental condition, tissue, or physiological response and promoter regions
determined for candidate genes using genomic DNA.
However, microarray analysis has some limitations. For example, this process
can be limited by the diversity of biological samples used to generate the complimentary
DNA (cDNA) libraries. The library developed may be limited by developmental
stage, tissue type, or growth condition; therefore, changes in gene expression are
restricted to the cDNA or expressed sequence tags (ESTs) isolated. Difficulty may arise
in sampling a particular cDNA library to sufficiently identify low abundance transcripts
and the use of genomic DNA over cDNA may increase the amount of hybridization with
pseudogenes. The utility of this approach is hampered by the number of genes that
exist in the database to which no known function has been assigned. Knowledge of the
complete genome of the organism being studied would be ideal to understand gene
expression such as Arabidopsis to reduce the number of unknown genes as well as
isolate promoter regions.
Microarray analysis has proven to be a powerful tool to study gene expression
and understanding the multiple response pathways that influence plant growth
and development. Prior studies generally investigated a single gene product during
stress and most often did not define the role of the stress-related gene stressing conferring
tolerance to the stress. Microarray analysis has broadened the analysis of gene
expression in response to a stress determining large scale changes in transcript profiles
associated with stress and has confirmed the results of the single gene studies (Seki et
al., 2001; Heath et al., 2002). Microarray analysis has been used to explore the role of
individual genes and groups of genes expressed in plant tissues at various growth
stages and under different environmental stress conditions (Fernandes et al., 2002).
Fernandes et al. (2002) conducted a comparative analysis of maize gene expression to
test the hypothesis that different structures express discrete sets of genes. The EST
libraries were developed from corn leaf primordia, 10-14 day old endosperm, 1-2 cm
immature ear, 4 day old root tissue, 1 mm tassel, greater than 2 cm tassel, mixed tassel
stages, mixed embryo stages, and mixed adult organs. As a result, each tissue and
development stage sampled in maize appeared to have a distinct set of moderate to
highly expressed genes from specific gene families. The use of microarray analysis is
not limited to the species the cDNA or ESTs were isolated from. Similar gene expression
results can be obtained from closely related species. Girke et al. (2000) developed