**6. Genome-Wide Association Study (GWAS)**

The advent of NGS technologies provides a large number of sequence variants (mainly SNPs) within a shorter period. These sequence variants can be utilized for QTL mapping, GWAS, and germplasm characterization. The establishment of an association between genotype and phenotype is a very challenging task. For crop improvement, it is necessary to determine the genetic basis of the agronomic trait. GWAS is a powerful technique for detecting natural variation and fine mapping of QTL underlying complex traits [174]. It requires a collection of individuals or a population of diverse genotypes and highly polymorphic markers that showed genome-wide distribution. This is a very robust method, in comparison to biparental cross-mapping, to map multiple traits simultaneously. In tomato, Shirasawa et al. [77] reported the whole genome resequencing of six tomato cultivars and detected 1.5 million SNPs by mapping the reads onto the reference genome (SL2.40). They utilized Illumina GoldenGate assay for genotyping of 1536 SNPs in 663 tomato accessions. There was no population structure observed when analyzing the genetic relationship using the STRUCTURE software. Further, they identified a total of nine SNP loci that were found to be associated with eight morpho‐ logical traits. To overcome the low polymorphism in cultivated tomato (*S. lycopersicum*), they used genome admixture of the cultivated and its wild ancestor (*S. pimpinellifolium)* for association mapping in tomato [175].
