Online Mendelian Inheritance in Animals (OMIA is a freely available information resource, which includes information for Equus inherited traits/diseases (collectively called phenes). The database focuses on Mendelian traits and their likely causal variants (mutations). Some of these Mendelian traits are favored by humans, e.g., coat color, while others are diseases. Additions to OMIA are based on publications of peer-reviewed research. Maintaining up-to-date information in OMIA is a challenge, owing to the multiplicity of species, the increase in the number of relevant publications, and as reference genomes and methods of citation continue to evolve. This challenge has been successfully aided by contributions from scientists from around the world. In some cases, those scientists are faculty members who charge their students with curation as an educational activity. Recently, OMIA has introduced computerized lists of standardized names and synonyms (called ontologies) for breeds of Equus and other animals and for phene categories. These ontologies facilitate increased connectivity between OMIA and other online resources. OMIA is and will continue to be a major reference resource for Mendelian phenes in the genus Equus.

Introgression is the transfer of genetic material between 2 different species via repeated back crossing of the interspecific hybrid and one of the parent species. These are important events to understand in the study of molecular evolutionary relationships between species. Previous studies have found regions of introgression within the horse genome, likely hundreds of thousands to millions of years ago from a non-caballine equid that are present in current horse populations. Our hypothesis is, these regions are retained among horses because they are doing something functionally beneficial and are increasing the horse's fitness. After identifying these regions with maximum likelihood estimation in a sample Thoroughbred population, the next steps were to analyze the different haplotypes found in modern horse genomes to find what polymorphisms were inherited together. Once identified, the genotypes of 230 Thoroughbred horse genomes were phased with BEAGLE. The positions tagged by BEAGLE were then viewed in Tassel 5 and a linkage disequilibrium plot was created. The phased genotypes were then analyzed, and the different haplotypes were extracted from the variant call file (vcf), taking into consideration the linkage disequilibrium plot and allele frequencies. Three main haplotypes occurred in this sample population: the reference, orTwilight, haplotype, the non-caballine haplotype, and another haplotype of unknown origin. This pipeline presents the number of haplotypes in the sampled population and which polymorphisms are inherited together, which gives us a better understanding of the origin on the introgressed haplotype(s). The short-term goal is to identify which non-caballine equid is the most prominent donor of the non-caballine haplotype. Ultimately, we will develop software to automate this analysis and identify putatively impactful introgressed regions using recently published data from the Equine-FAANG project. Currently, we are finding what the introgressed regions code for in the context of the horse genome, either non-coding RNA, a gene, or a non-coding region, to narrow down the search when putting together phylogenetic trees. Overall, the more we understand introgression, the better we will be able to piece together evolutionary relationships, how they are essential for rapid adaptation historically, and how they impact gene function in modern populations.

Centromeres are epigenetically specified by the histone H3 variant CENP-A. Although mammalian centromeres are typically associated with satellite DNA, we previously demonstrated that the centromere of horse chromosome 11 (ECA11) is completely devoid of satellite DNA. We also showed that the localization of its CENP-A binding domain is not fixed but slides within an about 500 kb region in different individuals, giving rise to positional alleles. These epialleles are inherited as Mendelian traits but their position can move in one generation. It is still unknown whether centromere sliding occurs during meiosis or during development. Here, we first improve the sequence of the ECA11 centromeric region in the EquCab3.0 assembly. Then, to test whether centromere sliding may occur during development, we map the CENP-A binding domains of ECA11 using ChIP-seq in five tissues of different embryonic origin from the four horses of the equine FAANG (Functional Annotation of ANimal Genomes) consortium. Our results demonstrate that the centromere is localized in the same region in all tissues, suggesting that the position of the centromeric domain is maintained during development.

Native Americans of the Plains and Rocky Mountains are renowned for their horsemanship. Taylor et al. recently used ancient DNA and other bioarcheological approaches to document how horses dispersed throughout America and transformed Native American societies following their introduction by the Spanish in 1519, well before the arrival of European settlers.

Equine arteritis virus (EAV) is the causative agent of equine viral arteritis (EVA), a respiratory, systemic, and reproductive disease of equids. Following natural infection, up to 70% of the infected stallions can remain persistently infected over 1 year (long-term persistent infection [LTPI]) and shed EAV in their semen. Thus, the LTP-infected stallions play a pivotal role in maintaining and perpetuating EAV in the equine population. Previous studies identified equine C-X-C motif chemokine ligand 16 (CXCL16) as a critical host cell factor determining LTPI in the stallion’s reproductive tract. Two alleles (CXCL16S and CXCL16r) were identified in the equine population and correlated with the susceptibility or resistance of a CD3+ T cell subpopulation in peripheral blood to in vitro EAV infection, respectively. Interestingly, CXCL16S has been linked to the establishment of LTPI in stallions, and thus, genotyping stallions based on CXCL16S/r would allow identification of those at the highest risk of establishing LTPI. Thus, we developed a TaqMan® allelic discrimination qPCR assay for the genotyping of the equine CXCL16 gene based on the identification of a single nucleotide polymorphism in position 1,073 based on NCBI gene ID: 100061442 (or position 527 based on Ensembl: ENSECAG00000018406.2) located in exon 2. One hundred and sixty horses from four breeds were screened for the CD3+ T cell susceptibility phenotype to EAV infection by flow cytometry and subsequently sequenced to determine CXCL16 allelic composition. Genotyping by Sanger sequencing determined that all horses with the resistant CD3+ T cell phenotype were homozygous for CXCL16r while horses with the susceptible CD3+ T cell phenotype carried at least one CXCL16S allele or homozygous for CXCL16S. In addition, genotypification with the TaqMan® allelic discrimination qPCR assay showed perfect agreement with Sanger sequencing and flow cytometric analysis. In conclusion, the new TaqMan® allelic discrimination genotyping qPCR assay can be used to screen prepubertal colts for the presence of the CXCL16 genotype. It is highly recommended that colts that carry the susceptible genotype (CXCL16 S/S or CXCL16S/r) are vaccinated against EAV after 6 months of age to prevent the establishment of LTPI carriers following possible natural infection with EAV.

Thoroughbred horses have been selected for racing performance for more than 400 years. Despite continued selection, race times have not improved significantly during the past 60 years, raising the question of whether genetic variation for racing performance still exists. Studies using phenotypes such as race time, money earned, and handicapping, however, demonstrate that there is extensive variation within these traits and that they are heritable. Even so, these are poor measures of racing success since Thoroughbreds race at different ages and distances and on different types of tracks, and some may not race at all. With the advent of genomic tools, DNA variants are being identified that contribute to racing success. Aside from strong associations for myostatin variants with best racing distance, weak to modest associations with racing phenotypes are reported for other genomic regions. These data suggest that diverse genetic strategies have contributed to producing a successful racehorse, and genetic variation contributing to athleticism remains important.

Most autosomal genes in the placenta show a biallelic expression pattern. However, some genes exhibit allele-specific transcription depending on the parental origin of the chromosomes on which the copy of the gene resides. Parentally expressed genes are involved in the reciprocal interaction between maternal and paternal genes, coordinating the allocation of resources between fetus and mother. One of the main challenges of studying parental-specific allelic expression (allele-specific expression [ASE]) in the placenta is the maternal cellular remnant at the fetomaternal interface. Horses (Equus caballus) have an epitheliochorial placenta in which both the endometrial epithelium and the epithelium of the chorionic villi are juxtaposed with minimal extension into the uterine mucosa, yet there is no information available on the allelic gene expression of equine chorioallantois (CA). In the current study, we present a dataset of 1,336 genes showing ASE in the equine CA (https://pouya-dini.github.io/equine-gene-db/) along with a work-flow for analyzing ASE genes. We further identified 254 potentially imprinted genes among the parentally expressed genes in the equine CA and evaluated the expression pattern of these genes throughout gestation. Our gene ontology analysis implies that maternally expressed genes tend to decrease the length of gestation, while paternally expressed genes extend the length of gestation. This study provides fundamental information regarding parental gene expression during equine pregnancy, a species with a negligible amount of maternal cellular remnant in its placenta. This information will provide the basis for a better understanding of the role of parental gene expression in the placenta during gestation.

Animal coloration is a complex, multifunctional trait that biologists have intensely investigated to unravel its proximate mechanisms and ultimate evolutionary drivers. Pigmentation is known to play a significant role in several aspects of fitness, including mate choice, camouflage/crypsis, defense/warning signaling, thermoregulation, communication, and immunity. Pigmentation genetics has been addressed in an extensive literature over more than a century, with some of the first studies being published in Journal of Heredity (e.g., Wright 1917, 1918), which has remained an important outlet for discoveries in this field. Throughout this period, some aspects of animal coloration genetics have become well understood, as discussed in several recent reviews (e.g., Hubbard et al. 2010; Cuthill et al. 2017; Alvarado 2020; Caro and Mallarino 2020; Orteu and Jiggins 2020; Eizirik and Trindade 2021). At the same time, many outstanding questions remain even on those aspects, whereas for other...

The present research aimed to characterize the Persian Kurdish horse population relative to the Persian Arabian and American Thoroughbred populations using genome-wide SNP data. Fifty-eight Kurdish, 38 Persian Arabian and 83 Thoroughbred horses were genotyped across 670,796 markers. After quality control and pruning to eliminate linkage disequilibrium between loci which resulted in 13,554 SNPs in 52 Kurdish, 24 Persian Arabian and 58 Thoroughbred horses, the Kurdish horses were generally distinguished from the Persian Arabian samples by Principal Component Analyses, cluster analyses and calculation of pairwise FST. Both Persian breeds were discriminated from the Thoroughbred. Pairwise FST between the two Persian samples (0.013) was significantly greater than zero and several fold less than those found between the Thoroughbred and Kurdish (0.052) or Thoroughbred and Persian Arabian (0.057). Cluster analysis assuming three genetic clusters assigned the Kurdish horse and Thoroughbred to distinct clusters (0.942 in cluster 2 and 0.953 in cluster 3 respectively); the Persian Arabian was not in a distinct cluster (0.519 in cluster 1), demonstrating shared ancestry or recent admixture with the Kurdish breed. Diversity as quantified by expected heterozygosity was the highest in the Kurdish horse (0.342), followed by the Persian Arabian (0.328) and the Thoroughbred (0.326). Analysis of Molecular Variance showed that 4.47% of the genetic variation was present among populations (P<0.001). Population-specific inbreeding indices (FIS) were not significantly different from zero in any of the populations. Analysis of individual inbreeding based on runs of homozygosity using a larger SNP set suggested greater diversity in both the Kurdish and Persian Arabian than in the Thoroughbred. These results have implications for developing conservation strategies to achieve sound breeding goals while maintaining genetic diversity.

This chapter describes the interaction of environment with genetics to generate phenotype in horses and highlights the methods for determining heritability and breeding values among horses.

This chapter presents a brief description of a few breeds of horses that will be mentioned in subsequent chapters. The descriptions includes population, landrace, related groups of horses, the relationship of the breeds to each other and the level of selection applied by breeders. Among the breeds that were presented in this chapter are Andalusian, Arabian, Belgian, Icelandic, Lipizzaner, Miniature, Norwegian Fjord, Paso Fino, Quarter horse, Shire, Standardbred, Tennessee Walking horse, and Thoroughbred.

This chapter describes the breeding of horses with specific coat colours and patterns and their genetic characteristics.

Abstract This chapter describes the genetic risk factors and mode of inheritance of hereditary diseases in horses.

Abstract 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.

Abstract This chapter describes the phenotypic and genetic characteristics of horse breeds with the leopard complex spotting coat colour and pattern.

This chapter describes the genetics of parentage testing in horses, including blood typing, DNA tests, genetic markers and other current and developing techniques.

Homozygous and compound heterozygous Miniature horses for ACAN alleles D1, D2, D3* and D4 exhibit chondrodysplastic dwarfism (OMIA 001271-9796). In a previous study, the carrier rate for these four alleles, combined, was 26.2%. The purpose of this study was to investigate whether carriers of these dwarfism-causing alleles had a shorter withers height than non-carriers. A total of 245 Miniature horses were tested for these four ACAN alleles and also were measured for withers height. Of these horses, 98 were carriers and 147 were non-carriers. A statistically significant difference of 1.43 inches was observed with the carriers being shorter (P = 1.72E - 11). The range of heights for the two groups overlapped, indicating that other factors, including genes, have an impact on withers height. However, the high carrier rate of these dwarfism-causing variants may be due to selection for decreased height.

Abstract This chapter describes the evolution, taxonomy, genetics and conservation of domestic and wild Equus species.