Abstract
Identifying diversity at many scales is the keystone to understand how genomes evolved and plants are so adaptable, even if they are under extreme constraint. Understanding the processes that create diversity and how the genome manages this variability is of high importance to be able to face today's challenges for breeding and genetic resource conservation of crop plants. For about past 15 years, we ushered into the era of pangenomics and started to learn what the true intra-species genomic diversity is and how it shapes the structure and the expression of the genome, especially in crop plants. The pangenome is the complete repertoire of sequences for a given population (often a species). It can be divided in compartments, the first one is the core genome which contains the sequences shared by the whole population. The second compartment is the dispensable genome which regroups the sequences shared by some individuals of the population but not all of them. As a sub-part of the dispensable genome, an individual-specific-genome regroups the sequences that are uniquely found in one individual of the population. By comparing individual gene and sequence contents within a population, pangenomics is a great tool to investigate how sequences evolve within a species and how genetic diversity is shaped within it. More and more studies are including relative wild species to have a larger overview of how genetic and phenotypic diversity was shaped through domestication and selection processes. In this chapter, we will present this concept of pangenomics and the associated methods and progress made, particularly in crop plants and future perspective.