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

The first study based on GWAS showing the interaction of bacteria

P. syringae was performed in 2005 by Aranzana and colleagues (2005).

Recently, the enormous use of GWAS is due to the new technique developed,

i.e., NGS. This new technique is used for fine mapping of natural variation

using genetic markers (Bartoli & Roux, 2017). As tolerance to biotic stress is

the ultimate goal of breeders. A study done on hexaploid wheat plant under

different biotic stress has been reported in which 125 hexaploid wheat were

identified in providing resistance to fungal infections that causes various

diseases (wheat rusts and crown rot). The GWAS study confirmed the genes

and the genomic regions supporting resistance to biotic stress as 124 marker-

trait associations (MTAs) were estimated, out of which 33 of them were

found within the gene sequences. The result provided more insights into

stress resistance in wheat for future breeding programs (Bhatta et al., 2019).

10.6 ROLE OF NGS IN UNDERSTANDING PLANT RESPONSE TO

ENVIRONMENTAL STRESS

The next-generation sequencing or NGS technologies is a new technique which

includes Illumina/Solexa’s sequencing technology (San Diego, California,

USA) (Quail et al., 2008), and SOLiD sequencing technology, etc. NGS has

wide applications in the field of genomics like genome projects, transcriptome

analysis and RNA sequencing. The advance in NGS technology has enabled

researchers to identify gene networks of candidate genes that may response

to different environmental stress. The understanding of genetic variations

of secondary traits related to stress tolerance and identification of variations

in nucleotides helps breeders to improve crops efficiently. In recent years,

the role of GWAS in the detection of genes associated with developmental

processes like stress tolerance in plants has been explored with more clear

vision about the expression patterns under stress conditions in different parts

and stages of the plant (Yu et al., 2006). The NGS-based RNA-seq methods

for transcriptomes can help in the characterization of genes, detection of gene

expression, identification, and quantification of new transcripts and variation

in sequence of identified genes. Studies suggest that the response to various

stresses is controlled by a wide range of regulatory genes and their related

mechanisms. Transcription factors (TFs), other genes coding for transport

proteins that are somewhere involved in metabolic pathways and signaling

gets activated under stress conditions (biotic and abiotic) (Atkinson &

Urwin, 2012; Fan et al., 2013). However, unique genes are activated against