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Topic:Genetics
Genetics in horses encompasses the study of hereditary traits and the genetic makeup that influences various characteristics and health conditions in equine populations. This field involves the analysis of genes and their functions, inheritance patterns, and the impact of genetic variations on traits such as coat color, performance ability, and susceptibility to diseases. Research in equine genetics employs techniques such as genome mapping, sequencing, and genetic testing to identify specific genes and mutations associated with these traits. This page gathers peer-reviewed research studies and scholarly articles that explore the genetic basis of equine traits, the methodologies used in genetic research, and the implications for breeding, health management, and conservation of horse breeds.
Unveiling wolf dietary specialization on free ranging horses using forensic genetics and field monitoring. Wolves occasionally specialize on free-ranging horses when they are abundant and alternative prey is scarce, potentially reducing horse productivity, triggering conflicts with owners, and hampering conservation of both species. Yet, ecological and demographic impacts of wolf predation on horses remain poorly understood. We investigated wolf-horse interactions in NW Portugal by combining wolf monitoring, diet analysis, spatial overlap between wolf and horse activity areas, and horse pedigree reconstruction from genetically identified individuals recovered from wolf scat remains, feeding sites a...
Demographic change and selection patterns in thoroughbred racing horses over the 20th century. The Thoroughbred horse is a legacy of centuries of selective breeding for speed, emerging from the admixture of British mares and imported Oriental stallions. While previous work explored its genetic diversity, inbreeding, and selection signatures, the breed demographic and selection dynamics during the 20-century remain poorly understood. Here, we sequenced the genome of Phar Lap, a late-1920s/early-1930s racing champion, and analyzed the largest time-series of Thoroughbred whole-genome sequences, within a global panel of 850 horse genomes. Demographic modeling reveals a marked decline in gen...
Differential shaping of equine gut microbiota structure and function by breed and feeding regimen. The gut microbiota plays an essential role in host energy metabolism and immune function. Horses are non-ruminant herbivores that rely heavily on hindgut microbial fermentation to meet their energy requirements. However, the relative contributions of host genetic background (breed) and environmental factors (feeding regimen and geographical location) to shaping the equine gut microbiota remain poorly understood. Unassigned: In this study, 16S rRNA gene sequencing and functional prediction analysis were performed on 139 equine fecal samples to systematically investigate the differential effects...
Altered gene expression in the liver and small intestine of horses with equine neuroaxonal dystrophy. Equine neuroaxonal dystrophy/degenerative myeloencephalopathy (eNAD/EDM) is the second most common diagnosis of spinal ataxia in horses in the United States. The disease develops due to a combination of vitamin E deficiency and an unknown genetic risk factor(s), and there currently is no effective treatment. Objective: We performed transcriptomic profiling of the liver and small intestine of horses with and without eNAD/EDM, as both tissues are the main locations for absorption, metabolism, and delivery of vitamin E to the nervous system. Methods: Case-control exploratory study. Methods: Post...
Identification of a Novel Slow-Gray STX17 Lineage in Japanese Thoroughbreds via a Multi-tiered Copy Number Analysis Workflow. Gray is a dominant coat color phenotype in horses caused by a ~ 4.6 kb tandem triplication within intron 6 of syntaxin 17 (STX17). The copy number variation (CNV) of the duplicated segment influences the graying rate. The rare G2 allele (CNV = 2) is associated with a slower graying rate compared to the common G3 allele (CNV = 3) and is also relevant to melanoma risk. Current assays are limited because long and accurate PCR (LA-PCR) detects only the presence or absence of duplications, while droplet digital PCR (ddPCR) cannot reliably distinguish certain genotypes such as G3/g and ...
When genes meet money: Genotype-by-prize interaction in Quarter Horses. Barrel racing performance reflects a complex interplay among genetic merit, rider ability, training strategies, and competition-specific conditions. In practice, events differ substantially in their economic scale, and prize money can serve as a proxy for management intensity, rider expertise, and selection pressure. Objective: This study investigated whether economic stratification, represented by total prize money per event, is associated with changes in (co)variance components for barrel racing time in Brazilian Quarter Horses. Methods: A reaction-norm model was implemented using 349,262 ra...
Genes Associated With Fracture Risk in Thoroughbred Horses Have Novel Roles in Osteogenesis. Bone fractures in Thoroughbred racehorses are a major welfare problem. Genetic factors contribute to fracture risk. Cell models have previously identified 112 differentially expressed genes in bone-forming osteoblasts derived from horses at high and low genetic risk of fracture. However, 42 of these genes have no published role in bone. In this study, we identified novel roles for a subset of these genes in bone formation. Twenty-six of the 42 genes were expressed in Saos2 cells during basal culture and/or after 21 days of osteogenic culture. Five of these genes (ADSSL1, CABP1, ENO2, SPARCL1...
Genetic Indicators of Performance Resilience in Barrel Racing Quarter Horses. Resilience, defined as the capacity to maintain consistent performance under variable conditions, has emerged as a relevant breeding objective in livestock systems, yet remains largely unexplored in equine populations. The objectives of this study were to (1) derive indicators of resilience from longitudinal barrel racing time (BRT) records in Brazilian Quarter Horses, (2) estimate genetic parameters for these indicators, and (3) quantify their genetic relationships with BRT and accumulated career earnings (ACE). The dataset comprised BRT records from barrel racing events held between 2010 and...
Genomic diversity and historical legacy of Baroque horses: a living cultural heritage. Baroque horses represent a distinctive group of breeds that emerged mainly between the 16th and 18th centuries, shaped by the demands of European royalty and their courts. Although recognised as separate breeds, they share common ancestry, breeding goals, and historical gene flow. This study aimed to evaluate their genomic diversity, population structure, and admixture patterns. We analysed 1 160 individuals from eight breeds - Lipizzan, Old Kladruby Horse, Pura Raza Española, Lusitano, Friesian, Criollo, Peruvian Paso, and Puerto Rican Paso Fino - using 34 026 single-nucleotide polymorphis...
Factors Influencing Equine Embryo Outcomes in OPU‑ICSI Systems: Insights from a Large‑Scale Program in Brazil. Equine OPU‑ICSI supports commercial IVEP, yet substantial variability persists. We retrospectively analyzed a large dataset generated in Brazil spanning Quarter Horses, Warmbloods, and Mangalarga to evaluate whether predictors previously identified in the literature show comparable patterns under distinct ecological and breeding conditions. Overall oocyte and embryo outcomes were aligned with broadly reported trends from previous studies. Oocytes retrieved from estrous mares bearing a dominant follicle exhibited higher maturation and blastocyst rates. Stallion effects segregated into distinc...
Mitochondrial DNA reveals high maternal diversity within a weak breed structure in native Kazakhstani horses. Understanding the genetic diversity and evolutionary history of domestic horses () is essential for reconstructing their population dynamics and origins. In this study, we analyzed mitochondrial DNA variation (COI and cytb) in six Kazakhstani horse populations representing four native breeds (Kazakh, Kostanay, Adai, and Mugalzhar) to assess genetic diversity, population structure, and evolutionary relationships within a broader phylogenetic framework. High haplotype diversity combined with low nucleotide diversity revealed population expansion and admixture. Population structure analyses revea...
Thoroughbred horses susceptible to Recurrent Exertional Rhabdomyolysis have elevated skeletal muscle mitochondrial capacities. Recurrent Exertional Rhabdomyolysis (RER) is a skeletal muscle disease that can intermittently impede careers of equine athletes. Manifesting as episodes of muscular stiffness and degeneration, RER causes lost training and competition days. RER is associated with abnormal intracellular calcium (Ca) regulation. Calcium released from the sarcoplasmic reticulum to initiate contraction may also be transported into mitochondria, which impacts energy production. RER-susceptible horses exhibit down-regulated mitochondrial proteins but upregulated mitochondrial genes. Thus, mitochondrial function may ...
Genome-Wide Characterization of the TGF-β Gene Family in Donkey (Equus asinus) Reveals Lineage-Specific Gene Duplications and Deleterious Mutations. The transforming growth factor-beta (TGF-β) superfamily regulates diverse biological processes, including proliferation, differentiation, apoptosis, tissue remodeling, and reproductive signaling across metazoans. Here, we performed a genome-wide characterization of the TGF-β gene family in donkey (, ASM1607732v2) using comparative genomics and bioinformatics analyses, with horse (, EquCab3.0) as a reference to investigate evolutionary conservation and functional divergence. Genome assemblies and proteomes were retrieved from NCBI, and TGF-β genes were identified using BLASTp and HMMER searc...
Genetic Diversity in Domestic Horses: Temporal Patterns, the Influence of Assisted Reproductive Technologies, and Implications for the American Quarter Horse. Genetic diversity is the heritable variation within and among populations and is essential for the long-term health and selection potential of domestic horses. Previous studies show diversity across breeds is shaped by effective population size, founder events, artificial selection, and levels of inbreeding. While some closed-studbook breeds retain moderate genetic diversity, others have experienced rapid losses due to popular-sire effects and recent and extensive inbreeding. Even so, mare lines continue to help maintain genetic diversity within these populations. Assisted Reproductive Technol...
Identification of Genomic Differences Resulting from Selection in Iranian Kurdish and Turkmen Horse Breeds Using Single Nucleotide Polymorphisms. Breakthroughs in genomic technologies have enabled the formulation of methods to identify genomic variation in domestic animal species. Detection of the variation is necessary because it is associated with breed characteristics and economic importance in domestic animal genetics. Unassigned: This study aimed to identify the genomic regions in Turkmen and Kurdish horse breeds that have been the target of different selections over many years. It also sought to locate the genes and Quantitative trait loci (QTL) in these regions that contributed to the differentiation of these two breeds or the di...
Vietnam’s Horse Sector: A Comprehensive Review of History, Production Systems, Health Challenges, and Research Priorities. Horses in Vietnam have a long historical presence and continue to hold economic, socio-cultural, and medicinal importance across diverse regions. Despite these roles, comprehensive scientific information on equine development, including health and disease patterns, reproductive performance, genetic resources, and biomedical applications, remains limited and fragmented. In this review, we summarize existing knowledge on equine populations, production systems, and their development in Vietnam, as well as their roles in cultural practices, livelihoods, and traditional medicine. We then identify m...
Advanced paternal age is associated with reduced reproductive success and offspring racing performance in Australian Thoroughbred racehorses. Reproductive ageing influences fertility and offspring fitness across mammals. In humans and model organisms, paternal age has been associated with changes in sperm quality and genomic integrity, including oxidative stress, DNA damage, and epigenetic alterations; however, these mechanisms have not been directly examined in large equine populations. Thoroughbred racehorses provide a system to investigate paternal age effects at scale using detailed breeding records. In this retrospective observational study, with data from 35 retired stallions and 33,546 progeny, we assessed associations betwee...
Polygenic Prediction of Equestrian Sport Discipline Among Horses Bred for Jumping and Dressage. Horses bred for different equestrian sports vary in physical, physiological and behavioural requirements. Characterising genetic markers associated with discipline provides an opportunity to improve identification of horses best suited to either jumping or dressage. Using a composite selection signals test, genomic regions under positive selection in German warmblood horses divergent for discipline were identified that contained lead SNPs proximal to or within genes with functions relevant to the requirements for jumping and dressage. Dressage genes function in tortuosity of movement (GRM5) an...
Transcriptomic and Meat Quality Differences in Longissimus Dorsi Muscle of Surgically Castrated Three-Year-Old Kazakh Horses. Although the Kazakh horse is a dual-purpose breed renowned for both milk and meat production, the extent to which surgical castration alters gene expression in its muscles has not yet been fully elucidated. In this study, left longissimus dorsi muscle (LDM) samples were obtained from six Kazakh stallions (W group) and six Kazakh geldings (S group) to comparatively evaluate meat quality parameters, examine histological characteristics in tissue sections, and apply transcriptomic profiling to comprehensively explore the principal regulatory pathways and candidate genes through which surgical cas...
A Comprehensive Analysis of the Agreement and Performance of Variant Annotation Programs in Equine Genomes. Advances in whole-genome sequencing (WGS) technology have led to the widespread adoption of WGS for investigating genetic diseases and traits in domestic animals. This has created a need for improved methods for prioritizing candidate causal variants. One way variants are prioritized is using variant annotators that predict variant effects based on their proximity to genomic features and effect on amino acid sequence. However, validation of variant annotators for domestic animal genomes is lacking. In this study, we calculated the agreement of three popular variant annotators, Ensembl Varian...
Phenotypic characterization through identification of gait and coat color phenotype of the Mountain Pleasure Horse. Phenotypic characterization of traits like gait and coat color is useful for minor breed identification and conservation. The Mountain Pleasure Horse (MPH) is a minor American breed as it is listed as threatened by the Livestock Conservancy. Objective: The study objective was to utilize phenotypic characterization for identifying gait and coat color phenotype of the MPH. Methods: Gait was characterized utilizing frame-by-frame analysis to identify spatiotemporal variables of purebred horses (n = 6) performing the flat walk and saddle rack. Coat color was characterized using coat color assi...
Integrative Advances in Equine Genomics From Reference Assemblies to Evolutionary History and Key Traits. Horses are major domestic animals and cultural symbols that have accompanied humans for millennia. They underpin transport, agriculture, warfare and sport, and also provide a model for studying domestication, complex traits and adaptive evolution. Recent work in equine genomics has now generated a much richer picture of how these roles are grounded in the genome. This review brings together advances in several connected areas: the construction and refinement of reference assemblies; genomic reconstructions of origin, domestication and dispersal; global and regional patterns of genetic diversit...
Chromosomal chaos: understanding aneuploidy associated with assisted reproductive technologies. Pregnancy loss remains a significant challenge for the equine breeding industry, with substantial economic and management consequences. Chromosomal abnormalities have emerged as a central driver of pregnancy loss, particularly during early gestation, highlighting the need to better understand the etiology of this inherent genetic instability. Concurrently, the rapid expansion of assisted reproductive technologies (ART) offers promise for improving equine reproductive efficiency alongside the traditional practice of natural cover. However, the increasing use of in vitro embryo production (IVP) ...
Prevalence and Genetic Characterization of Giardia duodenalis and Blastocystis sp. in Horses in Shanxi Province, North China. (synonyms and ) and sp. are prevalent zoonotic intestinal protozoans with significant public health and economic importance. Both parasites infect various hosts, including humans and most livestock. can cause infections ranging from asymptomatic carriage to clinical manifestations such as acute diarrheal disease, growth stunting and malabsorption, whereas sp. infection is often asymptomatic and its pathogenicity remains debated. Following the rapid expansion of modern equine industries (horse racing, equestrian sports, production, and tourism), concern about the spread of parasitic diseas...
Prevalence, molecular characterization and zoonotic potential of Cryptosporidium spp. in horses from diverse husbandry systems across four provinces of northern and eastern China. Cryptosporidium is an obligate intracellular zoonotic protozoan causing diarrheal disease in humans and animals globally. Horses have more frequent close contact with humans through equestrian sports, breeding, and cross-regional trade. However, comprehensive molecular epidemiological data on diverse equine husbandry systems in China are limited. We tested 412 fecal samples from horses across four Chinese provinces via small subunit ribosomal RNA (SSU rRNA) nested polymerase chain reaction (PCR). C. parvum and C. equi were subtyped using the 60 kDa glycoprotein (gp60) gene, and C. andersoni ...
Sport predispositions in warmblood horses: insights from Grand Prix competitions. The aim of this study was to pilot the assessment of sport predispositions in warmblood horse breeds, both domestic and foreign, and to evaluate factors influencing their performance. Data from 293 horses (725 starts) competing in national Grand Prix events with obstacle heights of 140-145 cm were analysed using general mixed models. The origins of Polish Halfbred Horses were examined, and correlations between results in the Young Horse Championships and later Grand Prix performance were assessed. Results showed that performance is significantly influenced by genetic factors, such as breed and...
A Breed-Specific SNP Panel With Higher Theoretical Exclusion Power and Practical Equivalence to International Standards for Parentage Testing in Pura Raza Española Horses. Accurate parentage assignment is essential for managing livestock breeding and genetic improvement. This study evaluated a breed-specific SNP panel (375 SNPs) for the Pura Raza Española (PRE) horse, comparing its performance against the traditional STR reference panel (18 microsatellite) and the international ISAG SNP core panel (378 SNPs) across population scenarios differing in levels of inbreeding and kinship. The PRE-specific SNPs were selected from the Axiom EQUIGENE array based on high genotyping reliability (call-rate > 99%), Mendelian error minimization, Hardy-Weinberg equilibr...
Towards a Comprehensive Screening Approach for Detecting Gene Doping in Racehorses and Sport Horses by Targeting Common and Intrinsic Plasmid Sequences. The evolution of biotechnology and gene therapy has unfortunately facilitated the emergence of gene doping. Those misused applications are prohibited in equestrian sports (International Equestrian Federation (FEI)) and in horseracing (International Federation of Horseracing Authorities [IFHA]), reflecting major concerns regarding horse welfare and the integrity of competitions. Among the biotechnological tools that could be misused, eukaryotic expression plasmids represent a particular threat due to their ease of production, customisable design and ability to carry a wide range of performance ...
The “gait keeper” mutation does not influence gait scores in Pêga donkeys: a preliminary result. The DMRT3 "gait keeper" mutation is a major determinant of locomotor patterns in horses, but its role in donkeys remains unclear. This study evaluated the association between this polymorphism and gait performance in Pêga donkeys, a breed selected for gaited locomotion. A total of 260 animals were phenotyped for gait scores and genotyped by PCR-sequencing targeting exon 2 of DMRT3. All individuals were homozygous for the wild-type allele (CC), and the mutant A allele was not detected. The monomorphism precludes any association with gait scores, possibly indicating that this DMRT3 mutation has...
Machine learning-based gait classification and genome-wide association identify a QTL for gait type in Colombian paso horses. Coordinated mammalian locomotion relies on spinal circuits where regulates strides and alternative gaits. However, does not explain differences between the Colombian paso horse breed's specialized gaits, Colombian trocha and Colombian trot. We used inertial sensors and machine learning to develop accurate phenotyping ( = 225 horses), before performing genome-wide association analysis ( = 85 horses, 670K array). We identified a 2.43 Mb quantitative trait locus (QTL) on ECA16, where haplotypes featuring lead variants (rs1147402472, = 1.95 × 10; rs1136628503, = 8.52 × 10) explained 48.6% of...
