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

Functional Genomics of Stress Tolerance
305
quantitative analysis of global gene expression in rice using 9-11 bp fragment tags. In
rice seedlings, a total of 10,122 tags from 5921 expressed genes were analyzed and most
of the tags belonged to the category of highly expressed housekeeping genes.
Matsumura et al. (1999) also observed that among differentially expressed genes between
anaerobically treated and untreated rice seedlings, metallothionein and globulin
genes were highly expressed, and prolamin gene was most highly inducible. Eight
genes, including six showing no match to any rice EST, were anaerobically induced and
six genes were repressed. Global gene expression in rice leaf and seed revealed that
out of 50,519 SAGE tags, 15,131 tags corresponded to unique transcripts and 70%
occurred only once in both libraries (Gibbings et al., 2003). SAGE technology has also
been used in soybean (Schupp et al., 2003) and tomato (Mysore et al., 2001) to analyze
plant-pathogen interactions.
In Arabidopsis, SAGE technology was used to analyze changes in gene
expression in leaves (Jung et al., 2003) and pollen (Lee and Lee, 2003) undergoing cold
stress. A comparison of SAGE tags derived from cold-treated and normal leaves revealed
that genes involved in cell rescue/defense/cell death/aging, protein synthesis,
metabolism, transport facilitation and protein destination were highly expressed and
photosynthesis genes were down-regulated. In case of pollen, twenty-six out of 21,237
were expressed at least 10-fold more in cold-treated compared to normal pollen. Out of
highly expressed genes (more than 8-fold), only two genes were previously known to
be involved in stress responses or defense but, there is no direct evidence that the
function of these genes is related to cold stress.
By comparing the quantitative gene expression profiles of more than 10,000
tags between blast fungal (Magnaporthe grisea) elicitor- and buffer-treated control
rice cells, 139 putative elicitor-induced genes and 154 repressed genes have been identified
(Matsumura et al., 2003). Interestingly, 100 tags and 46 tags from elicitor-induced
and -repressed genes could not match with the rice cDNA and EST data base reflecting
on the need for enrichment of EST database. Among the down-regulated genes in the
elicitor-treated cells, Bl-1 gene coding for Bax inhibitor was identified. The expression
of Bl-1 is known to be involved in defense response in Arabidopsis (Sanchez et al.,
2000) and barley (Huckelhoven et al., 2003).
2.3. Microarray
Microarray technology has revolutionized the analysis of global gene expression profiling.
This technology is based on the principle of selective and differential hybridization
of nucleic acids. Two types of microarray are mainly used, i.e. oligonucleotide
based chip and cDNA microarray. DNA are spotted on a glass slide (DNA microarray)
or on to a nylon membrane (DNA array) using the pin-based fluid transfer or inkjet
dispensers (Fodor et al., 1991; Blanchard et al., 1996). Linker system to covalently
immobilize modified nucleic acids (Beier and Hoheisel, 1999) or ATMS/diazotization
technique (Dolan et al., 2001) can also be used to spot the DNA onto polypropylene