Concept of Pangenome and Its Application in Crop Plants

With the advancement of Next Generation Sequencing technology, databases have increased exponentially, resulting in the development of a new discipline, Comparative Genomics. Again, with the wide use of Comparative Genomics, another new discipline has been developed to study the full genetic diversity of a species. The discipline is called Pangenome, which is a combination of three subjects, mainly Genomics, Computational Biology, including Bioinformatics and Molecular Biology. In simple terms Pangenomics is the study of all genetic diversity present within a species or strains of a genus. In the construction of Pangenomics, DNA sequencing is the most important. For this reason, the technique of DNA sequencing has been developed to a large extent. Pangenome is constructed to compare easily with different strains or varieties of the same species or genus. The concept, discovery and application of Pangenomes in plants were discussed in this study. Plant genomes are dynamic with whole genome duplication, tandem duplication, transposable element duplication, chromosomal rearrangements or structural variations like deletion, inversion, translocation and recombination between species. Several methods have already been tried for the improvement of crop plants like Marker Assisted Selection (MAS), QTL mapping, Single Nucleotide Polymorphisms (SNP), Copy number variations and Genome Wide Association Studies (GWAS) by comparing with Reference Genome Assemblies representing the genome sequence of the genome of an individual or organism. But the Reference genome is not able to locate all genetic variations of a species. To overcome this limitation, the concept of Pangenomes may help in crop improvement, which has been discussed. Pangenomic studies have already been done in many crop plants like Rice, Wheat, Maize, Brassica, Soybean, etc. Some of these aspects were discussed. It is important to note that eukaryotic organisms are complex, with certain traits encoded not only by DNA but also by various forms of RNA. While pangenome analyses have already delivered significant benefits in crop science, incorporating both DNA and RNA sequencing into a complete pangenomic model may unlock even greater potential, not just in plant science, but also in animal and human genomics.