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Genetics and Microarray in Environmental Stress Response

8.2 ENVIRONMENTAL STRESSES AND METHODS FOR STUDYING

THE GENES THAT RESPOND TO THEM

Environmental stresses are the most important factors that reduce the perfor-

mance of agricultural products worldwide. Environmental stresses include

temperature, drought, salinity, flooding, quantity, and quality of light, atmo-

spheric CO2 concentration, soil nutrients, and heavy metal content (Chen

& Soltis, 2020). Resistance to environmental stresses is a quantitative trait

that controls many genes. To understand this trait, the gene network, which

includes various genes that are involved in controlling the desired traits

must be examined. The genes in a gene network definitely have common

cis-elements (CRM) and can have different cis-elements. Different datasets

are used to draw the gene network and high throughput methods are used to

evaluate the gene network.

There are different methods of determining the quantity and quality of

transcripts, which fall into three general categories:

•

Hybridization-based approaches:

¾ Northern blot;

¾ Microarray (Table 8.1).

•

PCR-based approaches:

¾ Quantitative PCR (qPCR);

¾ Real-time PCR.

•

Sequencing-based approaches:

¾ Sanger;

¾ SAGE;

¾ MPSS;

¾ RNA-Seq.

High throughput methods for studying gene expression in plants are

SAGE, DD PCR (differential display PCR), microarray and RNA-Seq. In

these methods, transcripts of many genes are examined simultaneously.

TABLE 8.1 Some of the Purposes of Performing Microarray

Types of Chips Target

Confirmation by

cDNA chip

Investigation of gene expression

Northern blot and real time PCR

DNA chip

Find SNP in DNA sequence

Southern blot

Protein chip

Testing a large number of proteins

Western blot