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

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FIGURE 10.3 Workflow of the process of next generation sequencing (NGS).

mapping takes advantage of linkage disequilibrium to find a link between

phenotypes and genotypes. The differentiation of genotypes is done on the

basis of molecular markers and phenotypes on the basis of traits in a refer­

ence set of germplasm. Theoretically, GWAS can be used in any germplasm

set for the identification of QTL that reveal variation in different traits

(Malosetti et al., 2007). A QTL is basically a part or region of DNA that is

related to some trait phenotype. The reason why GWAS is used is due to

its high-resolution mapping which provides greater capability in the identi­

fication of rare alleles by using statistical measures (Jin-long et al., 2012).

Different molecular markers like amplified fragment length polymorphism

(AFLPs) and SNPs are in use for mapping of QTLs which are further corre­

lated with the phenotypic data. With QTL mapping, there is an advantage

that different variants can be mapped in F2 generation of recombinant inbred

line (RIL). But this advantage also ends up with its limitation as the mapping