Genome-Wide Association Studies and Next-Generation Sequencing in Plant Response

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different stress (Atkinson & Urwin, 2012). Like for example, under heavy

metal concentrations, the plant withstands the situation by adopting some

common ways of defense which may include detoxification of excess heavy

metals. This detoxification process may include generation of ion sensing,

activation of metal transporter proteins and regulation of TFs as needed. The

regulation mechanisms and the genes associated with response to stress have

been effectively identified using NGS technologies.

Lead (Pb), being a toxic heavy metal, is accumulated by plants roots

which result in the entry of lead in the food chain which causes health issues

in human beings. In a study, NGS based-RNA sequencing was employed

to estimate the DEGs in radish plant and their effects under Pb stress were

examined (Wang et al., 2013). Another similar study has been reported on

Chromium (Cr) stress response in radish. The insufficient knowledge about

the molecular mechanism in response to Cr stress makes it more important

to be understood. In a study GWAS based RNA-Seq has been employed

in the identification of DEGs in response to Cr stress. The study resulted

in finding new insight to understand molecular mechanism in response to

Cr stress which helps in future manipulations in the genes for Cr accumu­

lation in radish plants (Xie et al., 2015). The microRNAs (miRNAs) are

responsible for growth, development, and response to environmental stress

in plants. The miRNAs are basically non-coding RNA sequences which are

single-stranded. The role of miRNA in heat stress response in radish has

been reported but their characterization is still unclear. So, as to understand

the effect of miRNA on target genes, Wang and colleagues (2015) identified

26 previously known and 19 new miRNAs under heat stress.

Phytophthora infestans (Mont.) is the causal pathogen to spread the

destructive disease in Tomato. Wild tomato is known to possess genes for

the resistance against this pathogen which could be used as a reference to

develop better breeds of tomato. To find such genes an identification study

has been done by Arafa and coworkers (2017) to find the candidate genes that

may provide resistance to tomato late blight by applying NGS technologies.

Two genes namely, Solyc06g083640.3 and Solyc06g071810.1 were taken

as candidates against resistance to disease. It was concluded that the SNP

and SSR markers linked to these two genes can be further used in marker-

based selection for breeding plants resistant to late blight disease. Betaine

aldehyde dehydrogenase 1 (BADH1), is a gene associated with salt stress

which is therefore involved in abiotic stress response. In the early stage of

germination, 475 rice accessions were used to investigate the association

of BADH1 haplotypes with accessions used in the experiment. In the result