The major histocompatibility complex (MHC) with its class I and II genes plays a crucial role in the immune response to pathogens by presenting oligopeptide antigens to various immune response effector cells. In order to counteract the vast variability of infectious agents, MHC class I and II genes usually retain high levels of SNPs mainly concentrated in the exons encoding the antigen binding sites. The aim of the study was to reveal new variability of selected MHC genes with a special focus on MHC class I physical haplotypes. Long-range NGS to was used to identify exon 2-exon 3 alleles in three genetically distinct horse breeds. A total of 116 allelic variants were found in the MHC class I genes Eqca-1, Eqca-2, Eqca-7 and Eqca-Ψ, 112 of which were novel. The MHC class II DRA locus was confirmed to comprise five exon 2 alleles, and no new sequences were observed. Additional variability in terms of 15 novel exon 2 alleles was identified in the DQA1 locus. Extensive overall variability across the entire MHC region was confirmed by an analysis of MHC-linked microsatellite loci. Both diversifying and purifying selection were detected within the MHC class I and II loci analyzed.

Clinical Department of Companion Leisure and Sport Animals INRAE VetAgro Sup Campus vétérinaire de Lyon Marcy L'Etoile France

Department of Animal Genetics Faculty of Veterinary Medicine University of Veterinary Sciences Brno Brno Czechia

Department of Animal Morphology Physiology and Genetics Faculty of Agronomy Mendel University in Brno Brno Czechia

Department of Parasitology and Parasitic Diseases Faculty of Veterinary Medicine University of Agricultural Sciences and Veterinary Medicine of Cluj Napoca Cluj Napoca Romania

Research group Animal Immunogenomics CEITEC VETUNI University of Veterinary Sciences Brno Brno Czechia

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