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

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the drought stress was given 343 differentially expressed genes (DEGs) were

identified in drought-tolerant group and 177 in the drought-sensitive group.

In the end, 7 putative genes were considered for further experiments and

also the results add on to knowledge regarding seminal root changes under

drought conditions in maize (Guo et al., 2020). Photosynthesis is an impor­

tant process in the life of the plant as it is directly linked to yield and produc­

tivity. Therefore, improvement in photosynthesis is important to increase

crop productivity. In a study, SNPs were found associated with different

parameters of photosynthesis including stomatal conductance (Cond), net

photosynthetic rate (Pn), transpiration rate (Trmmol) and intercellular carbon

dioxide concentration (Ci) by using GWAS in soybean. Around 219 soybean

accessions were exploited in which 12 QTLs linked to different traits like Ci,

Pn, Trmmol and Cond were disclosed (Wang et al., 2020). As GWAS is able

to do fine mapping of QTLs in a population, it is also used in plant response

to salt stress in the early stage of growth (vegetative). Nayyeripasand and

co-workers (2021) used more than 33,000 SNP markers to identify regions

in the rice genome associated with salt tolerance in vegetative stage.

There are several online tools available which help in integration of

GWAS and candidate gene information, understanding of pathways, interpre­

tation of genomic data, etc. TraitCapture is an online tool which helps in the

rapid identification of candidate genes, provides high throughput phenotypes

associated with genomes, next generation, and environment monitoring data.

It combines both GWAS and FSPMs to identify phenotypes in any particular

environment condition (Brown et al., 2014). Some other tools are available

for GWAS related data including PostGWAS, SNPinfo, PAST (Pathway

association tool), GMStool (GWAS-based marker selection tool, etc. (Xu &

Taylor, 2009; Hiersche et al., 2013; Thrash et al., 2020; Jeong & Kim, 2020).

10.5.2 BIOTIC STRESS

The appearance and re-appearance of plant pathogens bring deviation in the

process of both pathogen and host. It becomes necessary to understand the

genetic variations among the natural variations to know the adaptability of

the wild plant and make it feasible to improve breeding of resistant types.

The present time of genomics has led to the emergence of statistical tools like

GWAS important in understanding and discovery of novel genes associated

with desired traits which may include genes for resistance to environmental

stress. However, GWAS is not much used for estimation of genetic variants

in relation to pathogen resistance.