The germline holds the past and the future of a species, as parental genetic information is recombined through meiosis and transmitted to the offspring. Thus, understanding how the genome is organized and regulated in the nuclear space during the formation of germ cells is essential to comprehend the bases of fertility and its impact on genetic diversity. In the last twenty years, many studies have shown that in somatic cells, the genome is organized in chromosome territories which are formed by chromatin compartments folded into topological associated domains (TADs) and DNA loops. However, little is known about how the genome is organized in the germline and how chromosomal reorganizations modulate genome architecture. In this context, this thesis aims to: (i) understand the three-dimensional organization of the genome during mouse spermatogenesis and its interplay with gene function and occupancy of insulator proteins (CTCF and cohesins), (ii) investigate the implications of Robertsonian (Rb) fusions in genome folding and meiotic recombination, and (iii) characterize the variability of PRDM9 in natural house mouse populations with Rb fusions: the Madeira Rb system and the Barcelona Rb system (BRbS). We combined cytological analysis with next generation sequencing technologies, and we developed an efficient cell sorting protocol to obtain enriched germ cell fractions including spermatogonia, primary spermatocytes at early and late prophase I, round spermatids and sperm. Our results revealed that the higher-order structure of the genome is extremely dynamic during spermatogenesis, where spermatogonia presents somatic-like compartments and TADs, that disappear during meiosis to be re-established later on in post-meiotic cells. Moreover, transcription correlates with A compartments throughout spermatogenesis, with cell-specific active genes involved in spermatogenesis progression, fertilization and embryonic development. In addition, we found a correlation between cohesin occupancy and active transcription in both meiotic and post-meiotic cells, suggesting a transcription-regulating role of meiotic cohesins. Although germ cells with Rb fusions presented the main features of genome architecture, Rb fusions reorganize the spatial chromosome occupancy. In primary spermatocytes, Rb fusions increase heterologous interactions, promoting the formation of novel regulatory environments. In round spermatids, Rb fusions reduce inter-chromosomal interactions as a result of mechanistic constrains. The cytological data shows that the increase in heterologous interactions is concomitant with the presence of asynapsed heterozygous metacentrics, which induce the full heterochromatinization of the sex body. Furthermore, Rb fusions affect the number and chromosomal distribution of crossovers in primary spermatocytes, especially in the case of fused metacentrics in homozygosis. The reduction in recombination was also observed in the analysis of linkage disequilibrium based on SNP genotyping, which translated into high levels of genetic divergence in Rb populations when compared to standard mice. In addition, our characterization of PRDM9 variability detected an unprecedented variability in natural house mouse populations, being especially high in the insular Madeira Rb system when compared to the continental BRbS. Such differences could be attributed to the combination of different factors: (i) the evolutionary history of each Rb system, (ii) the prevalence of Rb fusions affecting genetic diversity, and to a lesser extent (iii) meiotic functional constrains (i.e., recombination hotspot asymmetry). Taken together, this thesis shows that chromatin undergoes profound remodeling during spermatogenesis in a cell-specific way, where transcriptional activity correlates with the chromatin state and cohesin occupancy. In addition, Rb fusions alter genome organization in the germline, having an impact on meiotic recombination and genetic diversity.