Polymorphism at expressed DQ and DR loci in five common equine MHC haplotypes

Abstract

The polymorphism of Major Histocompatibility Complex (MHC) class II DQ and DR genes in five common Equine Leukocyte Antigen (ELA) haplotypes was determined through sequencing of mRNA transcripts isolated from lymphocytes of eight ELA homozygous horses. Ten expressed MHC class II genes were detected in horses of the ELA-A3 haplotype carried by the donor horses of the equine Bacterial Artificial Chromosome (BAC) library and the reference genome sequence: four DR genes and six DQ genes. The other four ELA haplotypes contained at least eight expressed polymorphic MHC class II loci. Next Generation Sequencing (NGS) of genomic DNA of these four MHC haplotypes revealed stop codons in the DQA3 gene in the ELA-A2, ELA-A5, and ELA-A9 haplotypes. Few NGS reads were obtained for the other MHC class II genes that were not amplified in these horses. The amino acid sequences across haplotypes contained locus-specific residues, and the locus clusters produced by phylogenetic analysis were well supported. The MHC class II alleles within the five tested haplotypes were largely non-overlapping between haplotypes. The complement of equine MHC class II DQ and DR genes appears to be well conserved between haplotypes, in contrast to the recently described variation in class I gene loci between equine MHC haplotypes. The identification of allelic series of equine MHC class II loci will aid comparative studies of mammalian MHC conservation and evolution and may also help to interpret associations between the equine MHC class II region and diseases of the horse.

Microsatellite markers for evaluating the diversity of the natural killer complex and major histocompatibility complex genomic regions in domestic horses

“…For this reason, MHC microsatellite markers are commonly used for diversity studies not only in horses but also in sheep, platypus, cats, giant pandas, rodents, and even in fish . They allow assessing the extent of polymorphism not only for single loci but they also can be helpful for defining haplotypes . Genetic diversity of complex regions such as MHC or NKR can be inferred based on strong linkage disequilibrium observed in these regions in various species (reviewed by 11).…”

“…36,37 They allow assessing the extent of polymorphism not only for single loci but they also can be helpful for defining haplotypes. 24,38 Genetic diversity of complex regions such as MHC or NKR can be inferred based on strong linkage disequilibrium observed in these regions in various species (reviewed by 11). Several studies have showed that genetic diversity assessed by MHC-linked microsatellites correlated with data based on polymorphism of MHC genes.…”

Stallion semen quality depends on major histocompatibility complex matching to teaser mare

“…The horse's MHC includes several gene families with polymorphic loci that vary extensively in nucleotide diversity and in copy number of paralogous genes. Some of its molecular structure could recently be characterized, including several MHC class I (Tallmadge, Campbell, Miller, & Antczak, ) and MHC class II genes (Miller et al., ; Viļuma et al., ) of the Thoroughbred, Standardbred and the Arabian breeds. However, many MHC genes of other breeds are not sufficiently characterized at the molecular level, including several MHC genes of the Franches‐Montagnes breed we use here.…”

Embryo survival in the oviduct not significantly influenced by major histocompatibility complex social signaling in the horse

“…As in previous studies on horses [7][8][9][10] , a pair was classified as "MHC similar" if at least one ELA was shared between a stimulus stallion and a mare, and as "MHC dissimilar" if no ELA were shared. We decided against genotyping by MHC-linked microsatellites 54 because microsatellites are more likely to over-estimate variation in MHC structural genes than serological methods 55 .…”