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Topic:Genotyping
Genotyping in horses involves analyzing the genetic makeup of individual horses to identify specific genetic markers. This process aids in understanding genetic variations that may influence traits such as coat color, disease susceptibility, and performance capabilities. Genotyping can be used in breeding programs to select for desirable traits and manage genetic diversity within populations. Common methods for genotyping include single nucleotide polymorphism (SNP) analysis and microsatellite markers. This page compiles peer-reviewed research studies and scholarly articles that explore the methodologies, applications, and implications of genotyping in equine genetics and breeding.
Allele frequencies of 7 inherited disorders in performance and random cohorts of American Quarter Horses (2020-2024). To estimate allele frequencies for genetic diseases in the American Quarter Horse (QH), including hyperkalemic periodic paralysis (HYPP), type 1 polysaccharide storage myopathy (PSSM1), malignant hyperthermia (MH), myosin-heavy chain myopathy (MYHM), glycogen branching enzyme deficiency (GBED), hereditary equine regional dermal asthenia (HERDA), and equine juvenile spinocerebellar ataxia (EJSCA), and to compare these frequencies over time among elite performance subgroups and a random cohort of registered horses. Unassigned: In this prospective genetic survey, DNA was extracted from 300 elite ...
Comparative analysis of the karyotypes of Equus caballus and Equus asinus in the context of contemporary genomic data. Karyotypes of species within the genus Equus display considerable variation in chromosome number and are characterised by numerous structural rearrangements that have played a pivotal role in their evolutionary divergence and speciation. Equus caballus (horse), 2n = 64 and Equus asinus (donkey), 2n = 62, constitute particularly interesting models for comparative studies due to the diversified morphology of their chromosomes, including acrocentric and submetacentric pairs, documented Robertsonian translocations, and centric fusions. In recent decades, widely applied molecular cytogenetic techni...
First-time description of MHC diversity in Straight Egyptian Arabian horses using immune-linked microsatellite markers. Understanding the immunogenetic structure of the major histocompatibility complex (MHC) in Arabian horses helps to clarify the population health structure-related phenotypes of this historically influential breed. Straight Egyptian (SE) Arabian horses, which fall under , are of global value but are limited in number, raising concerns about their distribution and the genetic diversity associated with immunity. In this study, we examined 57 Egyptian Arabian horses from two breeding programs: one in Germany (AR-DE) and the other in Qatar (AR-QA). Sixteen polymorphic intra-MHC microsatellite marke...
Approaches to Thoroughbred Horse Identification in Diverse Sample Types Using Multiplexed SNP-PCR Sequencing Panels. The ability to determine the identity of equine samples would be highly advantageous in cases of ambiguous sample source, as individual-specific controls for gene editing detection, or forensic examination of suspect biological materials in potential doping cases. To this end, a SNP-PCR sequencing-based panel comprising 93 markers in one reaction was designed and investigated for use in Thoroughbred horses. Marker amplification performance and discriminating power were calculated against a population survey of 264 Thoroughbred whole blood samples from routine doping testing. The sensitivity of...
A Global Structural Variation Map Reveals Novel Variants for Body Conformation and Racing Ability in Horses. The selection of horses has been instrumental in shaping long-range mobility, advancing warfare strategies, and diversifying equine phenotypes. However, the structural variants (SVs) favored by this process remain largely unexplored. Utilizing high-fidelity Pacific Biosciences sequencing, we assembled three high-quality horse genomes, incorporating 237 Mb (9.48%) of novel sequences relative to the existing reference genome. These assemblies achieved an average Benchmarking Universal Single-Copy Orthologs completeness of 95.1%. By employing a graph-based approach, we genotyped 23,163 high-con...
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 ...
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...
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...
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...
Genetic diversity of horses of the Sargarinsko-Alexeevskaya and Irmen cultures of the Ob-Irtysh region of Western Siberia and their genetic proximity to modern horses of indigenous breeds. Genetic diversity of horses of the Sargarinsko-Alexeevskaya and Irmen cultures of the Ob-Irtysh region of Western Siberia and their genetic proximity to modern horses of indigenous breeds. Генетическое разнообразие лошадей саргаринско-алексеевской и ирменской культур Западной Сибири и их генетическое родство с современными лошадьми аборигенных пород.
Research Trends and Emerging Frontiers in Racehorse Genetics: A Bibliometric Analysis. The global horse racing industry relies heavily on elite breeding. Therefore, a molecular understanding of athletic traits is crucial for the industry's advancement. This study utilized Bibliometrix, VOSviewer, and CiteSpace to conduct a comprehensive bibliometric analysis of 869 publications in the Web of Science Core Collection (2011-2025), decoding the academic landscape and evolutionary trajectory of equine genetics. The results indicate a significant upward trend in academic output since 2019, with the United States, South Korea, and the United Kingdom emerging as the primary contributors...
Theileria equi sensu lato genetic diversity and phylogeny: new insights from mitochondrion, apicoplast and nucleus multilocus gene analysis. Equine piroplasmosis is a significant tick-borne disease with a global distribution. Among the two causative agents, Theileria equi has undergone numerous taxonomic reclassifications over time, reflecting advances in our understanding of its biology, molecular characteristics, and phylogenetic relationships. Formerly named Babesia equi, now classified in the Equus group apart from Babesia and Theileria species, its genus name will again certainly change. The genetic diversity also within T. equi lead to the renaming of one lineage as Theileria haneyi. Theileria equi should better now be consid...
Genetic Diversity and Population Structure in Seven Lipizzan Populations Based on Microsatellite Genotyping. Lipizzan horses, bred for over four centuries, represent a unique genetic, cultural and historic resource. This study assessed genetic diversity and population structure across seven European Lipizzan populations, with emphasis on the Bosnia and Herzegovina population. A total of 547 Lipizzan horses were genotyped using 12 microsatellite markers. The parameters of genetic variability, admixture level and migration rate were calculated. The mean number of alleles, effective number of alleles and Shannon's information index were 5.78, 3.24 and 1.31, respectively. The average fixation indices wer...
CXCL16-associated genetic susceptibility to equine viral arteritis in export-bound horses from Spain. Equine viral arteritis (EVA) remains a relevant health and economic concern due to the ability of some infected stallions to establish long-term persistent infection with equine arteritis virus (EAV). Allelic variation in the CXCL16 gene has been identified as a determinant of susceptibility or resistance to the carrier state, positioning genotyping as a useful tool for risk-based reproductive and health management. Objective: To characterise the distribution of CXCL16 genotypes in export-bound horses from Spain and to assess the utility of CXCL16 genotyping for EVA prevention and control. Met...
Genetic diversity of Toxoplasma gondii isolates from members of the families camelidae and equidae worldwide: a systematic review. Toxoplasma gondii is an apicomplexan parasite with a global distribution and significant public health and veterinary treatment implications. The present systematic review collates worldwide information on the genotypic diversity of T. gondii isolates infecting Camelidae (camels, alpacas, llamas, etc.) and Equidae (horses, donkeys, zebras, mules, etc.) and highlights their potential role as sentinels of environmental contamination and zoonotic spread. An exhaustive literature search of six electronic databases (PubMed, Web of Science, Scopus, ProQuest, Science Direct, and Google Scholar) from ...
Retrospective assessment of equine herpesvirus type 1 (EHV-1) genotype-associated clinical disease in Ontario. Equine herpesvirus type 1 (EHV-1) is an important viral pathogen in horses, associated with diverse clinical manifestations including fever, upper and lower respiratory disease, neurological signs, ocular disease, and abortion. Currently, EHV-1 variants (genotypes) are classified based on a single nucleotide polymorphism mutation of the open reading frame 30 (ORF30). Unassigned: The aim of this retrospective study was to evaluate the EHV-1 genotypes present in horses with various clinical presentations, including respiratory disease, abortion, and neurological disease, at a referral center in ...
Machine Learning-Based Genome-Wide Association Study Reveals Genetic Loci Associated with Body Measurement Traits in Yili Horses. Body measurement traits are key indicators for evaluating growth performance, production potential, and breeding value in Yili horses. However, studies investigating the association between body measurement traits and mutation loci in Yili horses remain limited. In this study, 255 adult Yili mares were used as the study population, including 152 speed-type and 103 meat-type individuals. Whole-genome resequencing was performed, and four phenotypic traits and body weight were measured. A mixed linear model (MLM)-based genome-wide association study (GWAS) was conducted using GEMMA (v 0.98.5), inc...
Additional Evidence Fails to Associate Variation in KCNE4 With Equine Anhidrosis. A prior genome-wide association (GWA; N = 200) including Thoroughbreds and stock horses implicated chromosome 6 (NC_009149.3) in owner-reported equine anhidrosis. A missense variant in KCNE4 (NC_009149.3:g.11813731A>G) was proposed as a risk allele, although its association with anhidrosis was not reported. Variant annotation and protein modelling in the original study suggested the G allele conferred risk. We reported no association of the G allele with anhidrosis in 50 horses phenotyped by an intradermal terbutaline sweat test (ITST); all horses produced sweat regardless of genotype. ...
Genomic diversity and structure in arabian horses revealed by whole-genome sequencing: establishment of an allele frequency database of common genetic variation. BACKGROUND: The Arabian horse is a culturally and historically influential breed that has contributed to the development of many modern horse populations. However, genomic resources for this breed remain limited, particularly population-level allele frequency datasets that support studies of genetic diversity, selection, and disease. The aim of this study was to generate a comprehensive allele frequency database for Arabian horses using representative sampling and high-coverage whole-genome sequencing. RESULTS: We generated the first publicly available allele frequency database for the Arabian...
Genetic diversity in the Criollo Argentino horse from SNP array data. The Criollo Argentino horse is a national symbol and a heritage breed that represents both cultural identity and a key component of traditional production systems in Argentina. This study aimed to assess the genetic differentiation of the Criollo Argentino relative to other horse breeds and to infer potential factors shaping its diversity through the genomic analysis of 24 representative animals. Samples were genotyped using a medium-density SNP array containing 65,157 markers, and genetic diversity analyses were conducted across autosomal SNP sets filtered under different criteria. Contempora...
HERDA-associated variant in bull-catching (vaquejada) Brazilian Northeastern bull-catching Quarter Horses. Bull-catching (vaquejada) accounting for approximately 13% of sport horses in Brazil. Genetic screening has enabled strategies to reduce the spread of inherited disorders, including Hereditary Equine Regional Dermal Asthenia (HERDA), a major skin disease included in the Six Panel required for registration by the Brazilian Quarter Horse Breeders Association. Although the HERDA-associated variant has been extensively studied in other disciplines, it had not been evaluated in Bull-catching Quarter Horses (QH). Objective: The present study aimed to determine the allele frequency of the pathogenic ...
Comprehensive molecular characterization of Theileria equi: Detection, genetic diversity, and risk factors assessment. Equine piroplasmosis, caused by Theileria equi, has been widely studied globally, but genetic diversity research in India remains limited. Analysis of 306 horse blood samples revealed T. equi infection in 10.78% by microscopy and 21.24% by PCR. Universal primers targeting 18S rRNA of T. equi and Babesia caballi were used, followed by species-specific primers generating 435 bp amplicons. Sequenced PCR-positive samples revealed high homology (99.52-100% in India, 95.89-100% globally), with all Indian isolates classified as genotype A. The EMA-1 gene phylogenetic analysis confirmed the insights f...
United States stakeholder insights on genetic testing for equine health and breeding. The S1094 United States Department of Agriculture Multistate Research Project is a collaborative effort utilizing equine genetics and genomics to improve horse health and well-being. It also provides educational resources and genetic testing tools to equine industry stakeholders. Objective: A survey assessed the knowledge, priorities, and information sources of U.S. horse owners and enthusiasts regarding equine genetic testing to inform future outreach and research efforts. Methods: An online survey was distributed from March to October 2024, targeting horse owners and enthusiasts across the U...
DMRT3 Gene Variations in Horse Breeds Selected for Gaited Movement – Established Research and Novel Findings. The DMRT3 gene, often referred to as the "gait keeper," plays a key role in controlling alternative gaits in horses, such as tölt and pace. This study aimed to determine the frequency of known and to screen for potential novel polymorphisms within the second exon of the DMRT3 gene. Methods: A total of 244 blood or hair samples were collected from representative individuals of the six horse breeds: gaited (Icelandic Horse, French Trotter), non-gaited (Arabian Horse, Malopolski Horse), and pony breeds (Welsh Pony, Shetland Pony). Methods: The second exon of the DMRT3 gene analyzed using Sanger ...
Unveiling genetic diversity in Egyptian Arabian horses (Equus caballus) through cytogenetic and ISSR marker analysis. This study combined classical cytogenetics and ISSR molecular markers to characterize genetic diversity in 24 Egyptian Arabian horses. Karyotyping revealed the standard equine chromosome number (2n = 64) with no numerical or structural abnormalities. Chromosome measurements were consistent with ISCN Equine standards: autosomal relative lengths (RL%) followed the expected size hierarchy, biarmed chromosomes displayed metacentric to submetacentric morphology (CI = 37-50%), and recalculated centromeric indices confirmed the presence of measurable p-arms on all acrocentric chromosomes. ISSR an...
An increased number of heterozygous calls in the AxiomTM Equine Genotyping Array. Single nucleotide polymorphism (SNP) arrays are commonly used in livestock genetics to investigate complex traits including genome-wide associations and fine mapping, genomic prediction and genetic diversity analyses. In a European equine diversity study, we analysed the AxiomTM Equine 670K SNP genotype data from 2,768 equids representing 20 horse breeds and one donkey breed. Using a strict detection setting to identify genome-wide runs of homozygosity (ROH), 169 purebred horses displayed fewer ROH segments than F1 crosses. Under medium and relaxed settings, ROH counts increased, while some ho...
Population Structure and Genetic Diversity Among Lipizzan Mare Families in Hungary Based on Microsatellite Genotyping. The conservation of genetic diversity in historically structured horse breeds requires fi-ne-scale population genetic evaluation beyond conventional pedigree-based approaches. The present study assessed genetic diversity, population structure, and mare family differentiation in a Lipizzan horse population using 16 ISAG/FAO-recommended microsatellite markers. A total of 172 mares representing 29 mare families were genotyped. All loci were polymorphic, with a mean number of alleles per locus of 6.69 and a mean effective number of alleles of 3.56. The average polymorphism information content (PIC...
Sex determination and genetic screening of equine embryos with whole genome amplification and real-time PCR. Reliable pre-implantation sex determination and genetic screening enables informed embryo transfer decisions in equine breeding while avoiding later interventions. We developed a streamlined workflow that couples rapid whole genome amplification (WGA) with a multiplex real-time PCR targeting ETSTY5 as a Y-specific marker and UBC as an autosomal control. On purified equine DNA, sex was correctly assigned down to 10 pg gDNA and to a single fibroblast cell. Direct testing of embryo biopsies without WGA yielded inconsistent results, whereas introducing a short WGA step produced tight allelic-discr...
Small Genome-wide association study of insect bite hypersensitivity in Hucul horses. Insect bite hypersensitivity (IBH) is a prevalent allergic skin disease in horses that significantly affects animal welfare and shows evidence of genetic predisposition. Objective: Understanding the genetic basis of IBH can improve management and breeding strategies. The Equine80K BeadChip microarray was used to identify genomic regions associated with the occurrence of IBH in Hucul horses. Methods: Hair samples were collected from 127 Hucul horses, including both affected individuals and controls. DNA was extracted and genotyped. A genome-wide association study (GWAS) was performed to identif...
