Genome-wide analysis of homozygosity regions in european simmental bulls

The study of Runs of Homozygosity (ROH) is a useful approach for the characterization of the genome of livestock populations. Due to their high relationship with autozygosity, ROH allow to make inference about population genetic history, to estimate the level of inbreeding, to assess within breed heterogeneity and to detect the footprints of selection on livestock genomes. Aim of this study was to investigate the distribution of runs of homozygosity in bulls belonging to five European Simmental populations and to assess the relationship between three production traits (milk yield, fat and protein contents) and autozygosity. ROH count, distribution and ROH-based coefficient of inbreeding (FROH) were calculated for 3,845 Simmental bulls of five different European countries: Austria (AT), Switzerland (CH), Czech Republic (CZ), Germany (DE) and Italy (IT). Average values of ROH number per animal, and total genome length covered by ROH were 77.8 ± 20.7 and 205 ± 74.4 Mb, respectively. Bulls from AT, DE and IT exhibited similar ROH characteristics. Swiss animals showed the highest (12.6%), while CZ the lowest (4.6%) FROH coefficient. The relationship between ROH occurrence and milk production traits was investigated through a genome-wide ROH-traits association analysis (GWRA). A total of 34 regions previously associated with milk traits (yield and/or composition) were identified by GWRA. Results of the present research highlight a mixed genetic background in the 5 European Simmental populations, with the possible presence of three subgroups. Moreover, a strong relationship between autozygosity and production traits has been detected.