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Genetics and Microarray in Environmental Stress Response

• Part II: Reaction Preparation: RNA is first extracted from the

target cells or tissues (under normal and stress conditions), and then

cDNA is synthesized. Labeling is performed during cDNA synthesis

using cy3 and cy5, which are fluorescents of different colors. The

cDNAs are then mixed and placed on a microarray chip to hybridize

with the oligonucleotide sequence placed on the chip (Southern,

1975).

• Part III: Analysis of Data: After hybridization, elution is performed

to wash labeled cDNAs that have not hybridized to a 25-nucleo­

tide sequence. Then bioinformatics scans and examinations are

performed (Southern, 1975).

8.4 LIMITATIONS OF MICROARRAY TECHNOLOGY

Controlling variability: DNA microarray is only for testing known genes. For

genes with low expression levels, the results of microarrays are significantly

different. To ensure that the obtained results are reproducible, and to reduce

the number of false positive results, it is always better to repeat. Sometimes

the total RNA is low and insufficient, and the amplification step needs to be

performed, which may cause bias (Chua et al., 2003).

In DNA microarray, variation hybridization occurs, meaning that a piece

of the well is hybridized elsewhere. It is difficult to normalize the results in

microarray technology; for example, the image quality obtained from wells

may be inadequate and the colors produced may be difficult (Varallyay et

al., 2008). Data retrieval from databases is difficult and its analysis requires

expertise.

8.5 EXAMPLES OF IDENTIFYING GENES IN RESPONSE TO ABIOTIC

STRESSES USING MICROARRAYS

A study has been conducted to investigate the effects of different combina­

tions of environmental stresses on the transcript level of the Arabidopsis

genome using microarray databases. Plants often respond to water deficiency

at the molecular and cellular levels, and a set of genes with different patterns

are induced or silenced (Shinozaki & Yamaguchi-Shinozaki, 2007).

Research has shown that the processes that lead to increased stress

tolerance and ultimately plant adaptation are regulated by signaling path­

ways. The result of activating these pathways is regulating the expression