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.
DURAN-JORDA F.This research article investigates the significance of eosinophil cells in horses and camels, focusing on the large granules found in these cells and their similarities to smaller red blood cells. […]
Nocera I, Moroni R, Fanelli D, Rota A, Di Franco C, Ungari C, Puccinelli C, Gandini M, Giusto G, Vannozzi I.Over the years, various diagnostic and surgical techniques have been developed to recognise and treat cryptorchidism in equid. This study retrospectively analysed cases of cryptorchidism referred to two centres between 2012 and 2025. Clinical data collected included species, breed, age, gender, location of retained testis, diagnostic approach, anaesthesia plan and surgical treatment, perioperative medical treatment, intra-operative complications and outcomes. A total of 37 clinical cases were included, 1/37 was a donkey and 1/37 was an intersex female. Most of the horses were three years old a...
Lewczuk D, Wypchło M, Hecold M, Buczkowska R, Korwin-Kossakowska A.Finding the causative mutations for musculoskeletal system development and health status is of a higher priority for all sport horse breeders' associations. Of the regulating proteins involved in animal ossification, 15 gene polymorphisms were chosen to be identified as connected with the nine fetlock and 14 hock bone structures measurements of 198 horses. All measurements were taken using X-rays of the limbs, which were available at the beginning and end of the horse training. The analysis of variance (GLM, SAS program) was performed taking into account identified training and horse-connected...
Berglund P, Andonov S, Strandberg E, Eriksson S.Harness racing is popular in several parts of the world, and the ability to race barefoot is an important trait for success because of its effect on racing time. Barefoot racing is also discussed in terms of animal welfare because not all horses have hooves that tolerate racing without shoes. In Swedish Standardbred trotters (SB) and Swedish-Norwegian Coldblooded trotters (CB), the proportion of barefoot races and the probability to race barefoot in any given race (barefoot status) have low-to-moderate heritability (h = 0.07-0.28). However, the genetic correlation between the ability to race...
Al-Ebshahy E, Badr Y, El-Ansary RE, Alajmi R, El-Ashram S, Rady A, Elgendy E.The present study investigated the molecular detection and genetic characteristics of equine herpesvirus 1 (EHV-1) and EHV-4 circulating within Egyptian horse populations during 2019-2022. A total of 79 animals were sampled (54 nasal swabs and 25 aborted fetal tissues). PCR assays revealed that 24 (30.3%) and 7 (8.8%) samples were positive for EHV-1 and EHV-4, respectively. Additionally, 5 (6.3%) samples were concurrently infected with both viruses. Four EHV-1 and three EHV-4 isolates were genetically characterized based on partial sequencing of gB gene. The four EHV-1 strains displayed 100% n...
Blomström AL, Hansen S, Riihimäki M.Papillomaviruses (PVs) are small, non-enveloped viruses with double-stranded circular DNA genomes that infect a wide range of hosts, including mammals, birds, reptiles, and fish. While human papillomaviruses are extensively studied, recent advancements in high-throughput sequencing techniques have increased the detection and genetic characterization of PVs from various animal species. Here, we describe the identification and whole-genome characterization of a divergent equine papillomavirus (EcPV) detected through a viral metagenomic investigation of a horse in Denmark exhibiting neurological ...
Ripollés-Lobo M, Perdomo-González DI, Azor P, Valera M.Investigate the genetic inbreeding depression load (IDL) on two dressage traits and two conformational defects in horses. Unassigned: The dataset included performance records for Walk and Points per Reprise (PPR) (N:43,838) and conformation data for Closed and Convergent hocks (N:57,949). Pedigree information spanned over 400,000 individuals. Inbreeding coefficients (F, F6, Fk) and partial inbreeding coefficient (Fij) were computed to quantify the IDL using Bayesian approach. Linear and ordinal logistic regressions were used to assess the relationship between inbreeding and phenotypic values. ...
Esdaile E, Houston K, Till BJ, Sutton RB, Scurrell E, Ling M, Hartley C, Bellone RR.Although several inherited ocular disorders have been extensively studied in horses, few reports of equine ectopia lentis exist and no genetic investigations have been reported. Ectopia lentis in humans and other species is reported to be caused by trauma, genetic variants, and systemic diseases. The most commonly reported genetic causes are dominant alleles in FBN1. Here we examined a 3-day old Oldenburg x Thoroughbred colt due to concerns over bilateral ocular anomalies and hypothesized that either a recessively inherited allele or a dominant de novo allele was the genetic cause. Examination...
Huang Q, Ren W, Shan D, Su Y, Li Z, Li L, Wang R, Ma S, Wang J.This study aimed to compare blood samples from Yili horses with outstanding and average performance in 5000 m races through transcriptome sequencing, identify key differentially expressed genes, lncRNAs, and circRNAs, as well as related enriched pathways, and elucidate their regulatory networks. This study used six healthy four-year-old Yili stallions as subjects, divided into an excellent group (E group, = 3) and an ordinary group (O group, = 3) based on their 5000-m race performance. Blood RNA-Seq technology was used to analyze differentially expressed mRNAs, lncRNAs, and circRNAs. A total...
Wang T, Yang X, Wang C, Wang J, Meng J, Yao X, Zeng Y, Ren W.Studying the genetic characteristics and molecular mechanisms of immune regulation in horses is of great significance for protecting their genetic resources, improving breeding strategies, and enhancing their disease resistance, thereby ensuring their healthy performance in both sports and production. Objective: This study investigates the genetic characteristics and molecular mechanisms underlying immune regulation in Yili horses, comparing them with Thoroughbreds and Kazakh horses. Methods: Blood samples from each breed were analyzed for physiological, biochemical, and immune indices alongsi...
Broothaers K, Angel-Velez D, Molto FLG, Hedia M, Coster T, Govaere J, Soom AV, Menten B, Smits K.In 2022, a repeatable protocol for in vitro fertilization (IVF) using fresh semen was established in horses. This facilitated successful capacitation of equine semen allowing to explore novel applications. Objective: We aimed to extend this technique to IVF with frozen-thawed semen and intracytoplasmic sperm injection (ICSI), and determine the outcome parameters such as blastocyst production and euploidy rates. Methods: A total of 221 oocytes were subjected to either IVF with frozen-thawed semen, ICSI with frozen-thawed semen incubated under capacitating conditions (ICSI cap) or control ICSI w...
da Silva GM, Navas C, Carvalho MB, Sampaio Y, Rocha MN, Gomes-Silva A, de Matos Guedes HL, Cunha L, Castilho LR, da Silva JL, Felicori LF.Horse immunoglobulins have been utilized for over a century in serotherapy to treat venomous animal bites and various other conditions. However, molecular-level information about these immunoglobulins remains limited, particularly regarding immunoglobulin lambda light chains (Igλ), which constitute over 90 % of circulating antibodies. Despite the sequencing of the equine genome, the International ImMunoGeneTics information system (IMGT) has not yet annotated Igλ in its database, restricting the analysis of the horse antibody repertoire. In this study, we analyzed the equine Igλ repertoire...
Jamshidpour R, Nabavi R, Moadab H, Rezaie F, Chale AC, Sargison N.Resistance to benzimidazole (BZ) by cyathostomin nematodes has become a major threat to equine health around the world. We aimed to evaluate the efficacy of BZ drugs against small strongyle nematodes in horses of western Iran using coprological and molecular examination. Unassigned: Faecal egg count reduction tests were performed on 398 horses kept in 16 stables in western Iran (Kermanshah Province), to detect benzimidazole resistance in small strongyle nematodes. Allele-specific PCR was used to identify the F200Y (TAC/TTC) SNP in the beta-tubulin gene codon in cyathostomin larvae. Unassigned:...
Hanousek K, O'Hara V, Riddell DO, Piercy RJ.In Thoroughbred horses, a highly prevalent short interspersed nuclear element (SINE) mutation in the myostatin gene (MSTN) promoter influences circulating myostatin concentration and is associated with muscle morphology, fracture risk and optimal race distance. Our prior data reveal that within horses there is substantial variation in serum myostatin concentration, particularly in MSTN heterozygotes and wild type horses but it was unclear whether such variation relates to within-horse differences or to environmental or temporal effects. Here we report the intra-horse consistency of circulating...
Taned M, Zandi MB, Salek Ardestani S, Abdoli M, Spangler ML.Race performance in Thoroughbred horses is influenced by both genetic and environmental factors. Understanding their genetic architecture is essential for designing effective breeding programs. Objective: This study aimed to estimate genetic parameters and trends for key performance traits in Iranian Thoroughbred racehorses. Methods: Performance data, including race completion time (RCT), rank at the end of the competition (REC), and average speed (AS), were obtained from the Iranian Equestrian Federation (2002-2021). Pedigree data from 14,391 individuals were analyzed using CFC software. Gene...
Moghbeli Damane M, Ayatollahi Mehrgardi A, Esmailizadeh A, Momen M.Inbreeding is caused by mating between related individuals and is associated with reduced fitness and performance. Generally, in the horse population, inbreeding is caused by geographically restricted areas and intensive natural or artificial selection. For this reason, assessing accurate inbreeding is essential for developing and implementing effective breeding strategies aimed at preserving genetic diversity and reducing the harmful consequences of inbreeding. One of the most accurate approaches for assessing genomic inbreeding and autozygosity is through the analysis of runs of homozygosity...
Encina A, Sánchez-Guerrero MJ, Ligero M, Rodríguez-Sainz de Los Terreros A, Valera M.White leg markings in horses are phenotypic traits influenced by genetic and environmental factors. This study analyzed their prevalence, symmetry, and genetic parameters in 38,825 Pura Raza Española (PRE) horses registered in the official studbook. White markings were scored using a binary (affected/unaffected) and a four-level ordinal scale. Most horses (38,341 out of 38,825; 98.8%) had at least one limb without white markings. The prevalence of white markings was higher in the hindlegs (17.9% LH; 14.5% RH) than in the forelegs (5.3% LF; 4.6% RF). Markings were most frequent above the fetlo...
Frontiers in geneticsNovember 12, 2025
Volume 16 1439312 doi: 10.3389/fgene.2025.1439312
Tang C, Yang B, Dawulietihan G, Xue L, Liu S, Yalimaimaiti Y, Wang Q, Yang N, Sun X, Wang Y, Wumaier A, Khizat S, Assanbayev T, Kozhanov Z....Xinjiang is a region renowned for its rich diversity of native horse breeds, making it one of the most affluent equine genetic resource areas in China. While prized for their high adaptability and tolerance to roughage, the conservation of these native breeds faces challenges from the introduction of external breeds and industrial changes. Furthermore, the unknown population structure of Xinjiang horse breeds has hindered effective conservation efforts. Unassigned: This study presents the first comprehensive Single Nucleotide Polymorphism (SNP) analysis of seven Xinjiang native horse breeds. W...
Donnelly CG, Peng S, Pflieger L, Manfredi J, Coleman M, Rappaport N, Price ND, Finno CJ.Metabolic syndrome (MetS)-encompassing obesity, insulin resistance, dyslipidemia, and hypertension-is prevalent in both humans and horses, offering a unique opportunity to explore shared pathophysiological mechanisms across species in a controlled model organism. In this first report from the Pioneer 100 Horse Health Project (P100HHP), we conducted a longitudinal, multi-omic analysis of 108 deeply phenotyped horses to interrogate individual health trajectories for precision insights into MetS. We identified two primary metabotypes: one characterized by elevated unsaturated triglycerides (TGs) ...
Chessari G, Reich P, Criscione A, Falker-Gieske C, Mastrangelo S, Tumino S, Bordonaro S, Marletta D, Tetens J.Single nucleotide polymorphism (SNP) arrays are commonly used for studying the genomic structure and diversity of livestock breeds, but whole-genome sequencing (WGS) provides higher-resolution genomic data. Genotype imputation has become a standard practice for increasing the genomic resolution of association studies. This work aimed to extend imputation to biodiversity analyses, comparing SNP array data before and after imputation. A 40 k SNP dataset of 281 horses from 12 breeds (DS) was imputed to sequence-level using a reference panel of 327 sequenced individuals, generating approximately 9...
Bhat S, Karunakaran S, Frossard JP, Choudhury B, Steinbach F.Equine arteritis virus (EAV) is the causative agent of equine viral arteritis, a notifiable respiratory and reproductive disease of equids that causes significant losses to the equine industry. This study presents a comprehensive analysis of two EAV outbreaks in the UK in 2019, combining virus isolation, sequencing and phylogenetic analysis to provide a holistic understanding of EAV dynamics in these outbreaks. Genetic characterization revealed that all outbreak strains were similar to viruses detected in the UK and Europe from 2004 to 2011, belonging to phylogroup D and clustering in two grou...
Mendoza Cerna MN, Anderson H, Avni G, Kahila Bar-Gal G, Juras R, Raudsepp T.Robertsonian translocations (ROBs) or centric fusions of acrocentric chromosomes are the most common structural chromosomal rearrangements in mammals. ROBs are of medical and veterinary concern because of associated subfertility and congenital disorders but are also of interest as a mechanism of chromosome and karyotype evolution. While ROBs are well documented in humans, mice, and cattle/bovids, they are extremely rare in horses, despite the 18 acrocentric chromosomes in the horse karyotype. Methods: We characterize the case using conventional and molecular cytogenetic approaches and DNA anal...
Song D, Wang G, Baterin T, Weng Y, Dugarjaviin M, Li B.Normal spermatogenesis in Mongolian horses depends on the mitotic division of spermatogonia, two successive meiotic divisions, and the morphological transformation of spermatids into mature spermatozoa. The gene is involved in the meiosis cycle and is required for normal chromosome association during meiosis. Previous studies have shown that alternative splicing of may promote spermatogenesis in Mongolian horses. In this paper, the regulatory effects of different alternative splicing events on Mongolian horse spermatogenesis are investigated. Results: In this study, two overexpressed lentiv...
Pepper B, North E, Culwell J, Nicodemus MC, Cavinder C, Harvey K, Williams T.Due to the incorporation of the Golden American Saddlebred Horse Association (GASHA) into the American Saddlebred Horse and Breeders Association (ASHBA), breeding for coat color has become more challenging for horse breeders. However, with this merger, pedigree tracing can be of value in pinpointing foundation bloodlines within the GASHA that influence production of the golden coat phenotype. Objective: The study objective was to document the historical origins of the GASHA through pedigree tracing to determine the influence of dilution alleles that produce the golden coat phenotype. Methods: ...
Harpke M, Brangsch H, Melzer F.In Germany, Contagious Equine Metritis (CEM) is a persistent problem in equine populations. The often subclinical nature of the disease, which is caused by the bacterium Taylorella equigenitalis, poses a problem for the breeding industry. However, there is a lack of knowledge about the genomic diversity of the pathogen in Germany, as studies on the genome level are lacking. Thus, in this study we sequenced 63 T. equigenitalis isolates from a strain collection and contemporary clinical isolates from before 2007-2024. Most of these isolates came from Icelandic horses in southern Germany. Based...
Kamiński S, Bejda J, Lewczuk D.The method for identifying the causative mutation for Warmblood Fragile Foal Syndrome (WFFS) involved PCR amplification of a 259-base pair fragment of the PLOD1 gene and its digestion with the restriction enzyme Aci I was developed, allowing for the clear detection of WFFS carriers. Eight WFFS carriers were detected among 308 warmblood horses kept in different farms across Poland, giving an overall frequency of 2.59%, which indicates a rather low frequency of the causative mutation for WFFS in Poland. Further research should be conducted on a larger number of horses, particularly those breeds ...
Sharma M, Singh A, Kumar V, Olla N, Arora R, Sharma R, Mohan NH, Ahlawat S.The genus Equus, encompassing horses, donkeys, and extinct relatives, has evolved over approximately 55 million years from small, multi-toed ancestors to the modern horse. Selective breeding has produced over 600 distinct horse breeds optimized for diverse traits such as size, conformation, performance, and adaptability. In the past two decades, rapid advances in equine genomics have significantly deepened our understanding of the molecular basis of these traits. The integration of high-throughput sequencing, genome-wide association studies (GWAS), and single-nucleotide polymorphism (SNP) geno...
Saldaña CL, Justo S, Murga L, Vásquez HV, Maicelo JL, Arbizu CI, Bardales W.The complete mitochondrial genome of the Peruvian Paso Horse was assembled using PacBio HiFi long reads, resulting in a high-quality circular genome of 16,617 bp comprising 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and a control region. Nucleotide composition and gene structure were consistent with other equine mitogenomes. Codon usage analysis revealed a bias toward CUA (Leu), AUA and AUC (Ile), suggesting translational optimization. Thirty-five heteroplasmic variants were identified, predominantly located in RNA genes (12 S rRNA and tRNA-Phe), with allele frequencies between 0.10 and 0.6...
Jlassi M, Dhifalli I, Ouled Ahmed H, Lasfar F, El Gtari M, Jemmali B.The genetic diversity and population structure of Tunisian Arabian horses were assessed using highly polymorphic microsatellite markers, which are critical for conservation and breeding programs. Despite the cultural and economic importance of Arabian horses in Tunisia, molecular data supporting their management remain limited. In this study, DNA from 130 horses was genotyped with 17 ISAG-FAO-recommended microsatellites to evaluate diversity within Eastern and Western Arabian lineages and their relationship to Thoroughbreds. Eastern Arabians showed an average of 5.176 alleles per locus, observ...
Atasoy MO, Turan T, Özbek R, Işıdan H, Naggar RFE, Afify AF, Rohaim MA.The genus (HCV) has long been a dynamic group, increasing its number by myriads of species collectively referred to as non-primate hepaciviruses (NPHVs). NPHV exhibits a broad hepatotropism and is often attributed to chronic infection in horses and dogs. However, recent studies and meta-analyses on NPHV in horses have remained inconclusive regarding the determination of risk factors for infection. Therefore, our main goal was to investigate the frequencies and molecular characteristics of NPHV infection linked to geographical location, horse breeds, genders, and ages. For this purpose, we tes...
Gmel AI, Haraldsdóttir EH, Rosa TV, Lamas LP, Neuditschko M, Weishaupt MA.Europe has many horse breeds differing in conformation, gaits and genetics due to diverging breeding goals. Research studies comparing objective gait parameters between different horse breeds are limited and date back a decade. Objective: In this study, objective gait parameters were measured in three European breeds, namely Lusitanos (LUS; n = 52), Franches-Montagnes (FM; n = 311) and Swiss Warmblood (WB; n = 40) using an inertial measurement system (sensors at poll, withers, pelvis and all four canon bones) at walk and trot. Results: At walk and trot, LUS moved significantly slower than WB a...
