Genomic variability of the MHC region: Empirical evidence from five horse breeds

•Forces shaping the genetic structure of populations can affect heterozygosity of usually highly polymorphic genomic regions such as major histocompatibility complex.•Despite differences in linkage disequilibrium between tested horse breeds, it appears that they share common genetic patterns regarding MHC class I and class II genes.•HRR islands and balancing selection footprints inside the MHC region indicated that they may be concentrated around class II genes. The purpose of this study was to analyse the level of variability in the autosomal genome, especially in the equine major histocompatibility complex region, in five horse breeds and identify heterozygosity-rich regions and potential footprints of balancing selection. Depending on data quality control, the dataset consisted of 51,168 or 53,874 single nucleotide polymorphism markers, available for 514 individuals (89 Lipizzan, 238 Old Kladruber, 47 Shagya Arabian, 61 Czech Warmblood and 81 Slovak Warmblood horses). Genomic variability within and between breeds was examined based on levels of heterozygosity (observed and expected), genomic inbreeding, Wright's FIS index and linkage disequilibrium. Subsequently, the screening of heterozygosity-rich regions and balancing selection signals derived from Tajima's D positive values was performed. As expected, due to the polymorphic nature of the major histocompatibility complex, the genomic variability level was generally higher when analysing only markers located in this area (mainly around genes belonging to class I). The Slovak and Czech Warmblood horses, as breeds with open herdbook, showed higher average values of heterozygosity indices than Lipizzan, Old Kladruber or Shagya Arabian breeds. Concerning only markers in the major histocompatibility complex region in complete or very high linkage disequilibrium, common patterns were found close to EQMHCB2, MHCB3 and EQMHCC1 genes belonging to class I and DQA1, DRB2, DRB3 and HLA-DOB genes from class II. Genome-wide, the number of heterozygosity-rich regions per animal ranged from 345.25 (Old Kladruber) to 603.33 (Czech Warmblood). Across all breeds, 254 heterozygosity-rich regions were detected directly in the major histocompatibility complex region (194 in class I and 60 in class II). Among them, the highest overlap showed regions found in the genomes of historically connected Czech and Slovak Warmblood breeds. The results suggested that the frequency of markers in heterozygosity-rich regions increased in