Genetic variation ranging from single-nucleotide polymorphisms to large structural variants (SVs) can cause variation of gene content among individuals within the same species. With the emergence of low-cost high-throughput sequencing technologies, numerous studies have shown that a single genome is not enough to identify all the genes present in a species. Recently, the pan-genome concept has become widely used to investigate genome composition of a collection of individuals. “A pan-genome refers to the full complement of genes of a biological clade, such as a species, which can be partitioned into a set of core genes that are shared by all individuals and a set of dispensable genes that are partially shared or individual specific. Pan-genomic data set has been developed for several crops using de novo assembly, meta-genomic-like and reference-based approach. Several pan-genomic tools available for Orthologous gene identification, SNP identification, Functional annotation, PAV identification and Profiling of pan-genome structure. Variations identified through pan-genome analysis can be used as markers for genomics assisted breeding. Pan-genomic studies offer a much broader understanding of genetic diversity of crop gene pools than re-sequencing studies and thus can be extremely useful in crop improvement. The super-pangenome is the approach of developing a pan-genome of the pan-genomes of different species for a given genus. The implementation of the super-pangenome concept will definitely boost GAB and will accelerate the crop improvement.