The linkage group formed by the ELA and A blood group system in horses was studied in American Standardbred horses. The distance between the ELA locus and the A blood group locus was measured as 1.61 centimorgans, observing only the haplotypes contributed by the sires. Strong linkage disequilibrium was found in pacing Standardbred horses for ELA-W1 with Aa, ELA-W5 with Ab and ELA-W10 with Ab. Linkage disequilibrium was apparent at both the population and family level. Among trotting Standardbred horses, linkage disequilibrium was found for ELA-W1 with Aa and for ELA-W10 with Ab. It was not possible to investigate linkage relationships in Thoroughbred horses because of the high frequency of Aa and low frequency of other A system markers.
Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory, systemic, and reproductive disease of horses and other equid species. Following natural infection, 10-70% of the infected stallions can become persistently infected and continue to shed EAV in their semen for periods ranging from several months to life. Recently, we reported that some stallions possess a subpopulation(s) of CD3+ T lymphocytes that are susceptible to in vitro EAV infection and that this phenotypic trait is associated with long-term carrier status following exposure to the virus. In contrast, stallions not possessing the CD3+ T lymphocyte susceptible phenotype are at less risk of becoming long-term virus carriers. A genome wide association study (GWAS) using the Illumina Equine SNP50 chip revealed that the ability of EAV to infect CD3+ T lymphocytes and establish long-term carrier status in stallions correlated with a region within equine chromosome 11. Here we identified the gene and mutations responsible for these phenotypes. Specifically, the work implicated three allelic variants of the equine orthologue of CXCL16 (EqCXCL16) that differ by four non-synonymous nucleotide substitutions (XM_00154756; c.715 A → T, c.801 G → C, c.804 T → A/G, c.810 G → A) within exon 1. This resulted in four amino acid changes with EqCXCL16S (XP_001504806.1) having Phe, His, Ile and Lys as compared to EqCXL16R having Tyr, Asp, Phe, and Glu at 40, 49, 50, and 52, respectively. Two alleles (EqCXCL16Sa, EqCXCL16Sb) encoded identical protein products that correlated strongly with long-term EAV persistence in stallions (P<0.000001) and are required for in vitro CD3+ T lymphocyte susceptibility to EAV infection. The third (EqCXCL16R) was associated with in vitro CD3+ T lymphocyte resistance to EAV infection and a significantly lower probability for establishment of the long-term carrier state (viral persistence) in the male reproductive tract. EqCXCL16Sa and EqCXCL16Sb exert a dominant mode of inheritance. Most importantly, the protein isoform EqCXCL16S but not EqCXCL16R can function as an EAV cellular receptor. Although both molecules have equal chemoattractant potential, EqCXCL16S has significantly higher scavenger receptor and adhesion properties compared to EqCXCL16R.
Summary. Six laboratories participated in the Fifth International Workshop on Lymphocyte Alloantigens of the Horse, testing 132 alloantisera against lymphocytes of 880 horses chosen to represent different families and breeds. Most of the alloantisera were produced by lymphocyte immunization between horses matched at the ELA‐A locus. All horses were also tested with antisera contributed to the workshop by participating laboratories which identified ELA specificities A1‐A10 and W12‐W21. Previously identified workshop specificities ELA‐W14, W15 and W19 were accepted as products of the ELA‐A locus based on family and population studies by the workshop. Their designations were changed to ELA‐A14, ELA‐A15 and ELA‐A19, respectively. Two new specificities were identified, namely ELA‐W22 (W22) and ELA‐W23 (W23). Population and family studies indicated that W22 and W23 as well as W13 are products of an ELA locus other than ELA‐A. The presence of these specificities was correlated with the presence of certain ELA‐A locus specificities, e. g. W13 with A3, W22 with A2 and W23 with A5. However, the association was not complete and W13, W22 and W23 also segregated with other ELA‐A specificities in some families. Evidence for recombination was found between the ELA‐A locus and the locus or loci encoding these specificities resulting in seven recombinant haplotypes found among the data presented in this workshop. Further studies are required for definitive assignment of the specificities to a class I or class II locus.
Summary. The Third International Workshop on Lymphocyte Alloantigens of the Horse was held on 25–27 April 1984 in Kennett Square, Pennsylvania. Twelve laboratories from five countries participated. The principal purpose of this Workshop was to determine the phenotypic and gene frequencies of the 10 equine lymphocyte antigens (ELA) and a non‐ELA lymphocyte antigen, ELY‐2.1, in several breeds of horse. A total of 86 alloantisera characterized in previous workshops were tested against lymphocytes from 1179 horses. In addition, several experimental antisera were also tested against the same panel of lymphocytes. As a result of analysis of these data, the Workshop recognized two new equine lymphocyte alloantigens: W11 of the ELA system, and ELY‐1.1, an antigen not linked to the ELA system.
Whole genome sequencing (WGS) samples. Whole genome sequencing samples with horse identification and read depth. 153 Individuals representing 24 breeds (Twilight is included as 4 entries). Table includes horse identifier, breed, contributing laboratory and coverage statistics for each individual in both the nuclear and mitochondrial genomes. Variant calling groups indicate which individuals were grouped together during variant discovery. (XLSX 21 kb)
This chapter discusses the approaches and recent findings by cytogeneticists on the abnormalities of horse chromosomes. Highlights focused on the following: sex chromosomes and autosomes, cytogenetics and genomics, variations in chromosome arrangements, diseases associated with gain or loss of autosomes, fertility problems associated with autosome rearrangements, disorders of sexual development, prevalence of chromosome abnormalities among horses and the future of clinical cytogentics.
This chapter describes the genetics of parentage testing in horses, including blood typing, DNA tests, genetic markers and other current and developing techniques.
