Various approaches for the genomic analysis of the genetic structure of different cattle populations

Runs of homozygosity (ROHom) and Runs of Heterozygosity (ROHet) are two techniques that allow the investigation of the genome and to study livestock population. Indeed, ROHom are continuous stretches of homozygous genotypes that are associated to autozygosity and to directional selection. ROHet, which are heterozygous chromosomal segments, can be due to balancing selection, where the genetic diversity is maintained via heterozygote advantage. In the first study, genotypes from 204 different breeds raised worldwide were investigated to observe differences in ROHom between different types of cattle (taurine, indicine, or hybrids) and between different geographical areas. The results confirmed that ROHom can be used to identify genomic signatures, in this case probably related to the environmental adaptation. In the second contribution, three different Italian dual-purpose breeds were genotyped to investigate ROHom and ROHet, and to test four different approaches for the ROHet detection, for which there is not consensus in the literature. Among the different approaches, two of them seemed to be more reliable, whereas the other two probably overestimated the number of ROHet. In general, less and shorter ROHet were found compared to ROHom. Moreover, the genes mapped inside these regions confirmed the hypothesis that ROHom are mainly linked to directional selection (i.e., production traits), and ROHet to balancing selection (e.g., environmental adaptation or fitness traits). Finally, in the third study, the effect of genotyping density and detection parameters was studied on ROHom and ROHet calling, using genotypes of Italian Simmental cattle. The results confirmed that the detection of ROHom was more reliable as long as the chip density increases, whereas the density impact on ROHet was not clear. Again, the highlighted ROHom mapped genes mainly linked to meat production traits, whereas in the ROHet there were gene involved in reproduction traits.