The plant cell nucleus is enclosed within the nuclear envelope harboring chromosome territories (CTs) and various nuclear bodies. It seems that the spatial organization of chromosomes is nonrandom and is characterized by many local and long-range contacts among genes and regulatory elements. Thus, it is evident that the architecture of interphase chromosomes plays a role in the regulation of gene expression. The introduction of sophisticated high-resolution microscopy and state-of-the-art genomics enables the complementary strategies to study CTs with high resolution. The aim of our project will be to characterize the spatial nuclear organization in interspecific hybrids and provides an insight into the positioning of chromatin from both parents using 3D-FISH. We sill evaluate the effect of parental genomes proportion on their positioning within the nucleus, track the dynamics in the genome organization during the cell cycle and reveal potential variation among different tissues. Our project will significantly increase our knowledge on the organization and function of hybrid genomes.