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.
BAER H, KABAT EA, KNAUB V.Blood group substances have been isolated from the saliva of human beings of blood group B and from the linings of individual horse stomachs. The properties of the human B substances are similar to those of hog and human blood group substances previously isolated. The horse substances showed lower hexosamine and reducing sugar and higher total and non-hexosamine nitrogen than do the materials from the other species. Materials isolated from individual horse stomachs possess either A or B activity or both. Certain stomachs yielded products of identical analytical composition but with neither blo...
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. […]
Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D.The core objective of racehorse breeding is to enhance the speed and endurance of the horses. The Grassland-Thoroughbred is an emerging horse breed developed in northern China in recent years, characterized by excellent speed performance, enduring stamina, and strong environmental adaptability. However, research on the genetic characteristics within this breed and the genes associated with athletic performance remains relatively limited. We conducted whole-genome resequencing of Grassland-Thoroughbred F1, F2, F3, and the crossbred population (CY) and obtained a total of 4056.23 Gb of high-qual...
Avila F, Esdaile E, Bellone RR. Standardbreds, a breed of horses used in harness racing at either the trot or the pace, established a closed studbook in 1973. Concerns about genetic diversity within the breed led the United States Trotting Association (USTA) to establish a limit of mares bred per stallion (i.e., a studbook cap) in 2009. Here, we aimed to evaluate the impact of the breeding restrictions on genetic diversity between and among subpopulations. : Sixteen short tandem repeats (STRs) were analyzed across a dataset of 176,424 Standardbreds foaled in the United States between 1998 and 2021. We examined allelic richn...
Scupham AJ.Many viruses mutate rapidly to adapt to host defenses, and for some of these viruses, the result is long-term infection in individual hosts. The work described here examines the infection and long-term maintenance of a newly identified virus, equine parvovirus-hepatitis (EqPV-H), in an individual horse. This description is possible because of a hypervariable region in the capsid gene; sequence variants were tracked by high-throughput sequencing of serum samples taken over a 16-year period. The data support the hypothesis that EqPV-H infection resulted in a sequence variant bottleneck. The cont...
Bazvand B, Rashidi A, Zandi MB, Moradi MH, Rostamzadeh J, Mahmoudi P.Iran is home to genetically distinct horse breeds shaped by geography and history. Breeds like the Kurdish, Caspian pony, and Turkmen reflect deep-rooted diversity and unique adaptive traits. Objective: This study aimed to identify genomic regions exhibiting signatures of selection and to detect candidate genes and biological pathways related to body size that may influence performance in various Iranian and exotic horse breeds. Methods: Samples were collected from three Iranian native breeds (Caspian pony, Turkmen, and Kurdish) and three exotic breeds (Fell pony, Arabian, and Akhal-Teke) orig...
Horses have inhabited Iberia (present-day Spain and Portugal) since the Middle Pleistocene, shaping a complex history in the region. Iberia has been proposed as a potential domestication centre and is renowned for producing world-class bloodlines. Here, we generate genome-wide sequence data from 87 ancient horse specimens (median coverage = 0.97X) from Iberia and the broader Mediterranean to reconstruct their genetic history over the last ~26,000 years. Here, we report that wild horses of the divergent IBE lineage inhabited Iberia from the Late Pleistocene, while domesticated DOM2 horses, nati...
Drögemüller M, Fouché N, Wyler M, Gurtner C, Meister SL, Neuditschko M, Jagannathan V, Gerber V, Leeb T.Hypertriglyceridemia (HTG) may be inherited and caused by variants in genes encoding enzymes of lipid metabolism. This study was prompted by the observation of eight Franches-Montagnes (FM) foals showing elevated plasma triglyceride levels and episodes of fatal acute pancreatitis. We termed this phenotype hypertriglyceridemia-induced pancreatitis (HIP). The affected foals were distantly related and inbred to a prominent stallion suggesting autosomal recessive inheritance. Whole genome sequencing of an affected foal identified a homozygous loss of function variant in LMF1 encoding lipase matura...
Corbally AF, Mulligan FJ, Sweeney T, Fahey AG.This study examines the associations between linearly scored phenotypic traits and auction sales prices of young event horses in Ireland, aiming to identify key traits influencing market value. Data from 307 horses sold at public auctions (2022-2023) were analysed using regression analysis, binary optimisation, and Principal Component Analysis (PCA). Regression identified Head-neck Connection, Quality of Legs, Walk length of Stride, and Scope as highly significant predictors of sales price ( < 0.001), with Length of Croup, Trot Elasticity, Trot Balance, and Take-off Direction also significa...
Santana ML, Bignardi AB, Faria RAS, Silva JAIV.Thermal load is a major welfare and performance concern for athletic horses, as physical exertion increases internal heat production. Although several phenotypic strategies have been developed to mitigate its effects, the genetic basis of thermal tolerance in horses remains largely unexplored. This study aimed to (1) evaluate the influence of thermal indices on the racing performance of Brazilian Quarter Horses, and (2) investigate the genetic basis of thermal tolerance through the estimation of genetic parameters across temperature gradients. We analyzed 21,857 racing-time (RT) records from 5...
Jafari H, Abebe BK, Cong L, Ahmed Z, Zhaofei W, Sun M, Muhatai G, Chuzhao L, Dang R.The domestication and selective breeding of horses have profoundly influenced the emergence of adaptive traits and stress resistance mechanisms, shaping modern equine populations. This comprehensive review examines the genomic foundations of these traits, emphasizing recent advancements in high-throughput sequencing technologies and bioinformatics. These tools have elucidated the genetic underpinnings of key characteristics such as endurance, speed, metabolic efficiency, and disease resistance. Importantly, the review identifies and connects gene variants associated with thermoregulation, immu...
Amaral TM, Ramos PDCA, Silva RA, Ferreira MM, Filho EDS.In the context of Brazilian equestrian sports, the Quarter Horse (QH) breed has the third largest population of registered horses and stands out for its numerous abilities in various disciplines. Studies on equine health and athletic performance parameters are scarce, especially involving molecular markers. Objective: This study aimed to investigate the differential expression of microRNAs and target genes involved in metabolic pathways of exercise and to assess hematological and clinical changes in 10 horses (Equus caballus Linnaeus) of the QH breed under different physiological conditions. H...
An T, Dugarjaviin M.(1) Background: The dun coat color, a wild-type phenotype in horses characterized by pigment dilution and primitive markings, is regulated by . This study explored the expression and localization of in the Bider marking (a primitive mark unique to the shoulder of horses); (2) Methods: We compared skin tissues from Bider-marked and non-Bider dun Mongolian horses. Samples were collected from the Bider area (dark-colored/light-colored shoulder), dorsal midline, and croup. Histological staining, qRT-PCR, and Western blotting were used to analyze pigment distribution and expression at mRNA and pr...
Shan D, Yao X, Ren W, Huang Q, Su Y, Li Z, Li L, Wang R, Ma S, Wang J.Whole-genome bisulfite sequencing (WGBS) was employed in this article to map blood DNA methylation profiles at single-base resolution in Yili horses before a 5000 m speed race, with comparative analysis of epigenetic differences between the 'elite group' and 'ordinary group' across six four-year-old stallions. The overall methylation level in the elite group was generally higher than that in the ordinary groups, with a minority of regions showing hypomethylation. For instance, the promoter regions of key metabolic and neuro-related genes exhibited significant hypomethylation. The article ident...
Pasicka E, Baca M, Popović D, Makowiecki D, Janeczek M.This study presents the sequencing and analysis of mitochondrial DNA (mtDNA) genomes from nine early medieval horse remains excavated across archaeological sites in Silesia region in present day Poland. Methods: Using aDNA extraction protocols optimized for short fragments, combined with target enrichment and high-throughput sequencing, we reconstructed partial mtDNA sequences for seven of the specimens. Results: The authenticity of the aDNA was confirmed through damage pattern analysis. Phylogenetic reconstruction revealed that the specimens belonged to six distinct mtDNA lineages (B, D, E, G...
Dao TTH, Szűts T, Duong NN, Troung DTQ, Solymosi N, Takács N, Hornok S, Farkas R.Equine piroplasmosis, caused by , and , significantly impacts on the veterinary and economic aspects of the global horse industry. However, many countries, including Vietnam, have not yet conducted epidemiological surveys to determine the prevalence of these haemoparasites. This study aimed to detect and/or infections in horses and to identify their genotypes. Blood samples were collected from 154 apparently healthy horses in eight districts of Hanoi, Thai Nguyen, and Son La provinces located in the northern part of the country. Twenty-four horses (15.58%, 95%CI: 10.70–22.14%) were found ...
Motta D, Aymée L, Roussouliéres I, Di Azevedo MIN, Jacob JCF, Lilenbaum W.Leptospirosis is a zoonotic disease caused by spirochetes of the genus Leptospira. Equine genital leptospirosis (EGL) has been described as a chronic and silent syndrome, presenting reproductive alterations such as abortion, stillbirth, placentitis, embryonic loss, repeat breeding syndrome, and subfertility. This study aimed to investigate the genital Leptospira infection in naturally infected mares with poor reproductive performance, as well as to genetically characterize the agents. A total of 41 mares with a history of poor reproductive performance were selected. Sera were collected for ser...
Gartland KL, Leśniak K, Twigg-Flesner A.Scientific interest in relation to Fragile Foal Syndrome (FFS) has proliferated in the last decade, but before this, many clinical cases were attributed to other similarly presenting equine neonatal disorders. It was thought that FFS-affected foals were mainly miscarried throughout gestation, but recent study results suggest that often, foals are born alive and die shortly after birth. FFS is proposed to have originated as long ago as the Godolphin Arabian, but the definite derivation of the mutant allele is unconfirmed. The discovery that FFS is present in 11-30% of Warmbloods and 2-3% of Tho...
Zhang C, Cai E, Ma Y, Zhong G, Gao Y, Wu Y, Liu B, Li J.This study investigated the cyathostomin species composition, anthelmintic efficacy, and potential resistance-associated mutations in Chinese grazing horses. Fecal samples were collected from 90 adult horses. Fecal egg counts (FECs) were determined using a modified McMaster method. Third stage larvae (L3) cultured from the eggs were identified to species level by PCR amplification and sequencing of the internal transcribed spacer-2 (ITS-2). The main species included and spp. However, differences in the relative abundance of less common species, including and , suggests regional variation. A...
Ivester K, Couetil L, Arora D, Wilkes R, Thimmapuram J.Fungal exposure is strongly implicated in the pathogenesis of asthma in horses, but the importance of specific fungi is unknown. Geographic variation in equine asthmatic endotypes is suspected and might be related to different fungal exposures due to different climatological and geographical conditions. This study had two objectives: evaluate the effect of the ecoregion upon BALF inflammatory cells and fungal community composition in horses with asthma and evaluate the effect of BALF fungal community composition upon the likelihood of neutrophilic, mastocytic and eosinophilic inflammation in t...
Armangau M, Lurier T, Josson A.Offspring Sex Ratio (OSR) at birth in mammals is generally assumed to follow a 1:1 male-to-female distribution, yet deviations in OSR have been observed and may be influenced by maternal and paternal factors. In this study we have focused on the effect of paternal factors (stallion age and breed) and breeding methods on the OSR. Using a retrospective dataset of 251,783 foal births recorded in France between 2015 and 2024, we applied generalized linear mixed models to evaluate the effects of these variables on the likelihood of producing a female foal. Stallion identity was included as a random...
Alonso MA, Dos Santos GR, Fonte JS, Marques PC, Pereira DD, Toral FLB, Bordignon V, Junior JB, Squires E, Fernandes CB.This retrospective study evaluated whether different reproductive biotechnologies influence neonatal behaviour parameters in foals. Data from 102 foalings in two commercial breeding farms were analysed, including foals conceived by artificial insemination (AI), conventional embryo transfer (ET) and intracytoplasmic sperm injection (ICSI). Neonatal parameters recorded were birth weight, time to achieve sternal recumbency, time to stand, time to nurse and time to meconium elimination. Mixed statistical models were applied to assess the influence of reproductive technique, breed, sex and farm. Si...
Derbala MK, Sargious MAN, Hagag NM, Pycock JF, Abu-Seida AM.Twin pregnancy in mares is one of the leading causes of abortions. Abortion invariably impacts both fetuses. This report describes an unusual case of a twin surviving to term following the abortion of its co-twin at 9 months in a 7-year-old Egyptian Arabian mare. At the time of abortion at 9 months of gestation, the size of the aborted fetus was equivalent to one of approximately 5 months of age while the age of the live co-twin was 9 months. Both fetuses were males. A skin sample was collected from the aborted fetus and hair samples were collected from the dam, sire and live foal for parentag...
Ramírez-Agámez L, Castaneda C, Hernández-Avilés C, Grahn RA, Raudsepp T, Love CC.Two methods for preimplantation genetic testing (PGT) have been described for equine embryos: trophoblast cell biopsy (TCB) or blastocoele fluid aspiration (BFA). While TCB is widely applied for both in vivo- and in vitro-produced embryos, BFA has been mostly utilized for in vivo-produced embryos. Alternative methods for PGT, including analysis of cell-free DNA (CFD) in the medium where in vitro-produced embryos are cultured, have been reported in humans but not for equine embryos. In Experiment 1, in vivo- (n = 10) and in vitro-produced (n = 13) equine embryos were subjected to BFA, cultu...
Hernández-Avilés C, Ramírez-Agámez L, Varner DD, Raudsepp T, Love CC.Cases of stallion subfertility due to acrosome dysfunction have been recognized since the 1990s. While some of these were observed in stallions with reduced sperm motility and morphology, a more severe form has been reported in stallions with normal-to-excellent sperm quality parameters, which is also uniquely observed in individuals of the Thoroughbred registry. These stallions carry a susceptibility genotype (A/A-A A in the gene FKBP6, exon 5) for Impaired Acrosomal Exocytosis (IAE). Current clinical observations from our group have identified a few highly subfertile stallions from other bre...
Asif S, Gulzar MW.Endometritis is a significant cause of infertility in mare. Some infectious agents disrupt the endometrium's innate immune system, resulting in a prolonged systemic inflammatory response that circulates via the blood or cellular degeneration, which ultimately leads to endometritis from bacterial endotoxins. Numerous biological processes use various small, non-coding RNA molecules called MicroRNAs. MicroRNAs (miRNAs) regulate gene expression after transcription by blocking transcription and translation. This manuscript examines patho-morphological discoveries in equine endometritis, the express...
Schwochow D, Alameddine A, Spörndly-Nees E, Montigny M, Naboulsi R, Jansson A, Niazi A, Lindgren G.Racing without protective shoes is common in the Swedish harness racing industry, as it can enhance horses' performance on the track. Trainers typically decide whether a horse will race barefoot based on practical experience rather than objective measures. However, this practice can sometimes lead to excessive hoof wear, posing potential welfare concerns for racing horses. Gene expression differences may help reveal the underlying genetic mechanisms associated with different phenotypic traits. To explore an objective measure for assessing which horses are best suited for barefoot racing, we co...
Hisaeda K, LE NAT, Kadekaru S, Ono T, Hiasa Y, Ohzawa E, Hata A, Kutara K, Sugimoto K, Une Y, Iwata E, Kunieda T, Zhang C, Kitagawa H.We evaluated metabolic abnormalities in six neonatal Noma foals (Nos. 54-57, 62, and 66) that died shortly after birth, using laboratory tests, pathological examinations, serum amino acid (AA) analyses, gas chromatography/mass spectrometry (GC/MS), and genetic analyses. Nonspecific clinical symptoms, such as poor suckling and weakness, were commonly observed at birth. Sepsis caused by various bacterial infections was detected in foal Nos. 54, 62, and 66, while a heart malformation was identified in foal No. 57. Laboratory tests showed high aspartate transaminase, lactate dehydrogenase, and cre...
Everts RE, Caron R, Foster G, McLoone K, Simiele L, Martin K, Brooks SA, Lafayette C.Roan coat color is described as the dispersion of white hairs within an otherwise solid background-color coat. This phenotype is primarily expressed on the body of the horse, with the head and legs exhibiting few or no white hairs. Previous studies mapped the locus for roan to the region and observed linked variants in a small number of breeds. Recently, we reported evidence for two independent haplotypes, and , in the region, which account for approximately 38% and 36% of roan horses, respectively. In the current report, using whole genome sequencing for unknown roan samples. We present a ...
Steensma MJ, Ducro BJ, Dibbits B, Doekes HP, van Schipstal JGC, Kalblfleisch T, Groenen MAM, Derks MFL.In horses, genetic diversity is predominantly observed between breeds, with little variation within breeds. The studbooks of the two largest horse populations in the Netherlands, the Dutch Warmblood horse and Friesian horse population, have ongoing conservation projects including collecting large-scale genotype and sequence data. The current reference genome, derived from a Thoroughbred horse can lead to bias in genetic analyses of other horse breeds. Therefore, the aim of this study was to create high-quality breed-specific reference genomes of Dutch Warmblood and Friesian horses. We performe...
Nemoto M, Kawanishi N, Kamei R, Furusho K, Kawauchi K, Yabuuchi Y, Oue Y, Uchida Y, Nishiura H, Reedy SE, Chambers TM, Li F, Bannai H, Yamanaka T....In April and May 2025, outbreaks of equine influenza occurred for the first time in 17 years in Japan. Equine influenza virus (EIV) of the H3N8 subtype was mainly detected in heavy draft horse populations in Kumamoto Prefecture and the Tokachi area of Hokkaido. In total, 10 EIVs were isolated from infected horses and then were used for genetic and serological analyses. Phylogenetic analysis of all eight genes revealed that all Japanese isolates were clustered with the Florida sublineage clade 1 (Fc1) viruses and were closely related to North American Fc1 viruses detected in 2024-2025. The resu...
Furukawa R, Tozaki T, Mizukami K, Iwasaki Y, Kawate K, Kikuchi M, Ishige T, Momozawa Y, Fukui E, Kakoi H.Thoroughbreds have been maintained as a closed breed for over 300 years since the crossbreeding between Arabian stallions and English mares. Despite interest in germline de novo mutations across species, their frequency in horses, particularly in Thoroughbreds, remains largely unexplored. Objective: This study aimed to identify de novo mutations in Thoroughbreds and estimate their frequency within a genetically closed population. Methods: We performed deep whole-genome sequencing (≥230× depth, 150 bp paired-end reads) and Sanger validation in a Thoroughbred trio (sire, dam, and foal). Reads...
