The three-dimensional organization of the genome in the nucleus is critical for many cellular processes. Hi-C is a newly developed, cutting edge method to analyze chromosome packing on a whole-genome scale using next-generation sequencing tools. Application of Hi-C to fungal and animal genomes has already revealed many new insights, providing a very high resolution picture of the nuclear arrangement of chromosomes. Given the different architecture of plant genomes, applying Hi-C to plants is very timely. Under the proposed project, Hi-C will be optimized for plant, and used to investigate the functional implications of chromosome packing in different genotypes and species. The first objective is to gain a comprehensive view of genome architecture in the model plant Arabidopsis thaliana, and to compare it to that of other organisms. The second objective is to take the advantage of high-quality whole-genome assemblies of different strains of Arabidopsis thaliana as well as of close relative, to ascertain the impact of small- and large-scale structural variation on chromosome packing. These data will be integrated with functional studies, to determine cause and effect between chromosome packing and genome features such as local transcription and chromatin modification. The third and final aim is to study how quickly chromosome packing responds to stress adaptation, as a first step towards understanding the role of chromosome packing in dynamic events.