Background Earlier next-generation sequencing technologies are being vastly used to explore, administer, and investigate the gene space with accurate profiling of nucleotide variations in the germplasm. Overview and Progress Recently, novel advancements in high-throughput sequencing technologies allow a genotyping-by-sequencing approach that has opened up new horizons for extensive genotyping exploiting single-nucleotide-polymorphisms (SNPs). This method acts as a bridge to support and minimize a genotype to phenotype gap allowing genetic selection at the genome-wide level, named genomic selection that could facilitate the selection of traits also in the pomology sector. In addition to this, genome-wide genotyping is a prerequisite for genome-wide association studies that have been used successfully to discover the genes, which control polygenic traits including the genetic loci, associated with the trait of interest in fruit crops. Aims and Prospects This review article emphasizes the role of genome-wide approaches to unlock and explore the genetic potential along with the detection of SNPs affecting the phenotype of fruit crops and highlights the prospects of genome-wide association studies in fruits.