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Biology and Biotechnology of Environmental Stress Tolerance in Plants, Volume 3

in or transformed this living system or the world of biology and that’s not

enough, it reorganized the biomedical world too. Representation of NGS

was very first showed up in 1996 (Ronaghi et al., 1996). This methodology

is highly developed, and currently, it is in use, and it is governing by various

platforms like Illumina and Life Technologies. The advanced sequencing

technologies reduces the expenditure of sequencing, on the other hand the

most up to date sequencing technologies not only lowers the sequencing cost,

also they are very quick which trim down the time required for sequencing

(Schuster, 2008; Tucker et al., 2009).

10.4.1 PRINCIPLE OF NGS

Principle of NGS is quite relatable to the previous sequencing technologies

or traditional sequencing, Sanger sequencing method that consider capillary

sequencing, is known as first generation sequencing. Generally, various NGS

stages embrace their own unique methodology of sequencing. Beginning of

NGS is done by preparing a template, the first step. And it all starts with a

Double-Stranded DNA material. Or we can say that DNA is the raw material.

Sources or isolation of this DNA material can differ. We can take different

DNA as sources they can be immuno-precipitated DNA, Reverse transcribed

DNA, or cDNA (Rizzo et al., 2012). The second step of this technique is the

preparation of library correspondingly. As we said that we use different DNA

so as their work also differs, and we use them accordingly. Fragmentation is

to be done into linear DNA molecules if we are considering genomic DNA

as a first step. cDNA is acquired in the making of linear DNA molecules, and

this is only possible or only done in the case of RNA where RNA is used in

the preparation by the help of reverse transcription (Figure 10.3). The major

differences between the first-generation sequencing and second-generation

sequencing are DNA fragments are used in lesser quantity, only one DNA

fragment is sufficient.

10.5 GWAS IN UNDERSTANDING PLANT RESPONSE TO

ENVIRONMENTAL STRESS

The common methods used for the detection of multiple traits in plants are

QTL mapping and GWAS. Quantitative trait loci (QTL) mapping is gener­

ally a statistical way to link two different sets of data including phenotypes

and genotypes. On the other hand, GWAS or linkage disequilibrium (LD)