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.
In this paper, we report a comprehensive and consistent annotation of the locus encoding the β-chain of the equine T-cell receptor (TRB), as inferred from recent genome assembly using bioinformatics tools. The horse TRB locus spans approximately 1 Mb, making it the largest locus among the mammalian species studied to date, with a significantly higher number of genes related to extensive duplicative events. In the region, 136 TRBV (belonging to 29 subgroups), 2 TRBD, 13 TRBJ, and 2 TRBC genes, were identified. The general genomic organization resembles that of other mammals, with a V cluster o...
Pepper B, North E, Foster M, Culwell J, Nicodemus MC, Cavinder C, Harvey K, Williams T.Registration numbers for the Palomino Horse Breeders of America (PHBA) have risen with the assistance of new registration guidelines. These changes in guidelines allowed for registration of any horse with a palomino body color, including those with unknown pedigrees. While this promoted registry growth, documenting the breed's orgins from those known pedigrees making up the breed's foundation is important with the introduction of unknown pedigrees. This can be accomplished using pedigree tracing, which is of particular value for color registries as the study of coat color patterns is plagued w...
Yoshihara T, Tozaki T, Nakaya S, Takasu M, Kawate K, Furukawa R, Kikuchi M, Isihge T, Nagata SI, Kakoi H, Hobo S.The Taishu horse is a native Japanese breed threatened with extinction. It is important to genotype the causative genes of rare phenotypes in endangered breeds because unique genetic traits might be lost unless a breeding strategy for conservation is constructed. In the present study, nine single-nucleotide variants and three indels of nine genes related to coat color, body composition, and gait were genotyped in 56 Taishu horses. Of these, only three genes were polymorphic. The observed coat color phenotypes coincided with the estimated phenotype from the genotypes, whereas black horses showe...
Liu YK, Fu WW, Wang ZY, Pei SW, Li KH, Wu WW, Le MZ, Yue XP.Chakouyi (CKY) horses from the Qinghai‒Xizang Plateau are well known for their unique lateral gaits and high-altitude adaptation, but genetic mechanisms underlying these phenotypes remain unclear. This study presents a comparison of 60 newly resequenced genomes of gaited CKY horses with 139 public genomes from 19 horse breeds. Population structure analyses (admixture, PCA, and neighbor-joining tree) reveal a close genetic relationship between CKY and other highland breeds (Tibetan and Chaidamu horses). Compared with other Chinese breeds, CKY horses present reduced nucleotide diversity (θπ)...
Cash CM, de Laat MA.The melanocortin 2 receptor (MC2R) has relevance to equine pituitary pars intermedia dysfunction (PPID), as it is the primary binding site for ACTH, which circulates at elevated concentrations in animals affected by PPID. Despite this, little is known about MC2R in equine species. The overall aim of this investigation was to determine MC2R mRNA expression in tissues relevant to PPID in healthy horses and to examine the MC2R gene sequence in a cohort of horses and ponies with and without PPID. The study found that the MC2R gene was expressed in both adrenal and pituitary gland tissues as report...
Guyo M, Tareke M, Tonamo A, Bediye D, Defar G.Morphometric traits discrepancies are associated with production, reproduction, adaptation and behaviours in horses. It also determines the design of harnessing implements, physical injury level and working performance of the native horses. Thus, the study was conducted to evaluate morphometric traits and body conformation indices of horse ecotypes reared across four districts of Bale Zone, Ethiopia. Methods: Data of croup height, croup length, hip height, mid-back height, wither height, hip width, thoracic depth, chest width, body length, sternum height, thorax perimeter and cannon perimeter ...
Mustefa A, Engdawork A, Sinke S.Ethiopian horses are multipurpose horses that have socioeconomic significance for smallholder farmers. However, studies regarding their husbandry practices have received little attention. Thus, the current study was conducted to assess the horse husbandry practices in the southwest Ethiopia. Data were collected through semi-structured questionnaires from a total of 196 randomly selected respondents. The general linear model and frequency procedures of the Statistical Analysis System (SAS 9.0) were used to analyze the quantitative and qualitative data, while indices were calculated using Micros...
Luan Y, Zhong L, Li C, Yue X, Ye M, Wang J, Zhu Y, Wang Q.Polydactyly was recorded before 100 BCE and attracted widespread interest because of its relationship to limb health and ancestral traits in horses. However, the underlying reasons for the development of polydactyly remain unclear. To search for polydactyly-related genes, we utilize a paternal half-sib family and screen for variants that match the mode of inheritance. Through this screening process, 77 variants in 65 genes are filtered. A missense variant (EqCab3.0 chr4: <107353368> A > G) (rs1138485164) in the 3rd exon of LMBR1 is identified as a source of amino acid sequence variatio...
Bussiman F, Richter J, Hidalgo J, Silva FFE, Ventura RV, Carvalho RSB, Mattos EC, Ferraz JBS, Eler JP, de Carvalho Balieiro JC.Gait visual scores are widely applied to horse breeding because they are a fast and easy phenotyping strategy, allowing the numeric interpretation of a complex biological process such as gait quality. However, they may suffer from subjectivity or high environmental influence. We aimed to investigate potential causal relationships among six visual gait scores in Campolina horses. The data included 5475 horses with records for at least one of the following traits: Dissociation (Di), Comfort (C), Style (S), Regularity (R), Development (De), and Gait total Scores (GtS). The pedigree comprised thre...
Benitez-Ibalo AP, Debárbora VN, Mangold AJ, Nava S, Sebastian PS.After the previous description and characterization of Theileria equi sensu stricto (Genotype A) in Argentina, the aim of the present study was to investigate the possible heterogeneity of 18 S rDNA genotypes circulating in this country. Therefore, blood samples from 18 horses from two different neighborhoods of Corrientes City, Corrientes Province, were analyzed for infection with Theileria species. Theileria DNA was detected in five samples (27.8%). Four nearly complete 18 S rDNA gene sequences were obtained and phylogenetic analyses were carried out. The maximum likelihood tree constructe...
Carvalho Serena G, Marchezan Piva M, Viezzer Bianchi M, Fernandes da Fonseca HC, Chitolina Pupin R, Martins Basso R, Secorun Borges A....In horses, systemic calcinosis is a rare syndrome characterised by muscle lesion associated with the mineralisation of large muscle groups or other organs, in the absence of an alternative cause for the calcification, such as toxic, enzootic or metabolic. Molecular and histopathological aspects of the disease are still poorly elucidated. Objective: To describe the epidemiological, pathological and molecular aspects of systemic calcinosis in a convenience sample of six horses submitted to necropsy in the Southern and Midwestern regions of Brazil. Methods: Retrospective exploratory study. Method...
Nykonenko A, Moturnak Y, McLoughlin PD.Understanding social relationships in at-risk species held in captivity is vital for their welfare and potential reintroduction. In social species like the Przewalski's horse (), daily time allocation and space use may be influenced by social structure and, in turn, reflect welfare. Here, we identify social relationships, time budgets, and spatial distribution of a group of nine older (aged 6-21 years) male Przewalski's horses living in a non-breeding (bachelor) group. We conducted our work at the Askania-Nova Biosphere Reserve, over 65 h of observation in summer, 2015. Horses formed stronger ...
Sharma NK, Singh P, Saha B, Bhardwaj A, Iquebal MA, Pal Y, Nayan V, Jaiswal S, Giri SK, Legha RA, Bhattacharya TK, Kumar D, Rai A.Copy number variations (CNVs) have become widely acknowledged as a significant source of genomic variability and phenotypic variance. To understand the genetic variants in horses, CNVs from six Indian horse breeds, namely, Manipuri, Zanskari, Bhutia, Spiti, Kathiawari and Marwari were discovered using Axiom™ Equine Genotyping Array. These breeds differed in agro-climatic adaptation with distinct phenotypic characters. A total of 2668 autosomal CNVs and 381 CNV regions (CNVRs) were identified with PennCNV tool. DeepCNV was employed to re-validate to get 883 autosomal CNVs, of which 9.06% were...
McGivney CL, McGivney BA, Farries G, Gough KF, Han H, Holtby AR, MacHugh DE, Katz LM, Hill EW.Equine recurrent laryngeal neuropathy (RLN) is an economically important upper respiratory tract (URT) disease with a genetic contribution to risk, but genetic variants independent of height have not been identified for Thoroughbreds. The method of clinical assessment for RLN is critical to accurately phenotype groups for genetic studies. Objective: To identify genetic risk loci for RLN in Thoroughbreds in a genome-wide association study (GWAS) following high-resolution phenotyping. Methods: Case-control. Methods: Thoroughbred horses were characterised as RLN cases and controls using resting a...
Myćka G, Ropka-Molik K, Cywińska A, Stefaniuk-Szmukier M.Among numerous genes that have been a focus of equine genetic research, the (Klotho) and (Alpha-actinin-3) genes stand out due to their significant roles in muscle function and overall health, as well as performance ability. Previous studies on Arabian horses and other mammalians have shown that both and occur in different isoforms that seem to have different roles in metabolism. The main purpose of this present study was to describe different isoforms (, , , , , ) expression levels affected by the endurance effort in Arabian horses. Methods: Blood samples were taken from a group of = 10 ...
Boozarjomehri Amnieh S, Hassanpour A, Moghaddam S, Sakhaee F, Ropka-Molik K.The gene is vital for fatty acid metabolism and is linked to environmental stress and physical exertion adaptation. The p.Asp237Ser variant (rs782885985) in is associated with increased enzyme activity and reactive oxygen species (ROS) levels. This study examined the polymorphism across six horse breeds in Iran: Arabian, Thoroughbred, KWPN, Caspian, Kurdish, and Turkmen. The goal was to identify differences in genotype distribution, potentially serving as genetic markers under selection pressure related to breed-specific traits. In a sample of 324 horses, genomic DNA was analyzed using PCR...
Stejskalova K, Vychodilova L, Janova E, Oppelt J, Horin P.Toll-like receptors (TLRs) play important roles in innate immunity and developmental processes. Due to their nature as molecular pattern recognition receptors, their genetic diversity may reflect the effects of various pathogen pressures. Here, the extent of variability in the TLR1-6-10 gene cluster in three geographically and historically distinct breeds of horses was analysed. A genetically diverse group of representatives of 14 other horse breeds provided additional information on the variability of this gene cluster in the domestic horse. Altogether, 25 SNPs were identified in the TLR6-1-1...
Kozak S, Merda D, Chesnais V, Breuil MF, Harrison M, Zdovc I, Golob M, Petry S, Duquesne F.Taylorella equigenitalis is the causative agent of contagious equine metritis, an internationally regulated sexually-transmitted infection in horses, which is of great concern as it usually results in temporary infertility. Taylorella asinigenitalis, the second member of the genus, is mainly found in donkeys and is considered non-pathogenic, although a first natural outbreak was reported in 2019 in the United Arab Emirates. Multilocus sequence typing (MLST) is currently used to study the epidemiology of Taylorella spp. but, while highly transposable and reproducible, it only focuses on < 0.5...
Heath HD, Peng S, Szmatola T, Ryan S, Bellone RR, Kalbfleisch T, Petersen JL, Finno CJ.Allele-specific expression (ASE) analysis provides a nuanced view of cis-regulatory mechanisms affecting gene expression. Results: An equine ASE analysis was performed, using integrated Iso-seq and short-read RNA sequencing data from four healthy Thoroughbreds (2 mares and 2 stallions) across 9 tissues from the Functional Annotation of Animal Genomes (FAANG) project. Allele expression was quantified by haplotypes from long-read data, with 42,900 allele expression events compared. Within these events, 635 (1.48%) demonstrated ASE, with liver tissue containing the highest proportion. Genetic var...
Durward-Akhurst SA, Valberg SJ.Several inflammatory myopathies have an infectious or immune-mediated basis in the horse. Myosin heavy chain myopathy is caused by a codominant missense variant in MYH1 and has 3 clinical presentations: immune-mediated myositis, calciphylaxis, and nonexertional rhabdomyolysis in Quarter Horse-related breeds. An infarctive form of purpura hemorrhagica affects numerous breeds, presenting with focal firm, painful muscle swelling, and subsequent infarction of multiple tissues. While Streptococcus equi equi is often the inciting cause, anaplasmosis, sarcocystis, piroplasmosis, viruses, and vaccines...
Baville E, Carstanjen B, Thomas-Cancian A, Calgaro A, Bonnet N, Tiret L, Gache V, Abitbol M.Supernumerary digits, or polydactyly, have been described in various species including humans, wild and domestic animals. In horses, it represents the most common congenital limb malformation, which has only been described in isolated cases or nuclear families. Molecular aetiology has not been reported. Objective: To characterise the phenotype of a non-syndromic pre-axial polydactyly in a horse family and to decipher the inheritance pattern. Methods: Retrospective study. Methods: Forty-three members of the family including a previously reported polydactyl case were recruited. Available clinica...
Ishikawa Y, Tufa SF, Keene DR, Bächinger HP, Winand NJ.Mutations in the collagen-modifying enzyme lysyl hydroxylase 1 (LH1) cause Warmblood Fragile Foal Syndrome (WFFS) in horses. We investigated the impact of this mutation on collagen structure and function. Our results show that LH1 deficiency leads to reduced lysine hydroxylation, altered collagen fibril organization, and tissue abnormalities resembling human Ehlers-Danlos syndrome. These findings highlight the critical role of LH1 in collagen biosynthesis and provide insights into the pathogenesis of WFFS.
Faulk C.Sequencing a genome by students has now become practical as we demonstrated with our recent publication of the Przewalski's horse (Equus ferus przewalskii) genome. In this review, I describe my experience teaching genome assembly in the classroom. In my course, students sequenced, assembled, and published a high-quality genome for Przewalski's horse using Oxford Nanopore long-read sequencing with only $4000 of materials. Along with the genome, we assembled the mitochondrial genome, sequence variants, predicted gene annotations, and DNA methylation levels. Our genome statistics far exceeded the...
Primo ALM, Assis DM, Santos VGS, de Melo LRB, da Nóbrega LD, Medeiros Dantas AF, Maciel TA.Cerebellar abiotrophy is a neurodegenerative disease that affects the Purkinje cells of the cerebellum, resulting in premature neuronal death. In horses, its occurrence has been reported mainly in the Arabian breed as a congenital mutation inherited in an autosomal recessive manner. The objective of this study was to describe the case of cerebellar abiotrophy in a Quarter Horse foal. An 8-day-old foal was treated after presenting signs of ataxia, hypermetria, difficulty maintaining a standing position, and decreased menace response. The foal was hospitalized for 26 days, received treatment wit...
van der Graaf L, Leigh W, Szmatoła T, Roberts K, Ryan S, Brown B, Van Buren S, Finno CJ, Petersen JL.Anhidrosis is defined as a decreased or absent ability to sweat in response to heat and exercise. In horses, this condition can increase the risk of life-threatening hyperthermia. A prior study has suggested that equine anhidrosis is associated with a missense variant (rs68643109) in the Potassium Voltage-Gated Channel Subfamily E Regulatory Subunit 4 (KCNE4) gene. This project aimed to validate this association in a population of well-phenotyped horses and to determine the allele frequency of this variant in publicly available whole-genome sequence data. Fifty horses within the University of ...
Fernandes TA, Paulino PG, Dos Santos Juliano D, Rabello CA, de Oliveira NVB, de Souza Santana M, Peckle M, Massard CL, da Costa Angelo I, Jacob JCF....Equine piroplasmosis (EP) is a reportable disease according to the World Organization for Animal Health (WOAH), caused by Babesia caballi, Theileria equi and T. haneyi. This syndrome is prevalent in tropical and subtropical regions, including various areas in Brazilian. This study examines EP in the Distrito Federal, Brazil, focusing on prevalence, epidemiological characteristics, and circulating genotypes. Epidemiological data and whole blood samples were collected from horses in the Distrito Federal. DNA was analyzed using qPCR for Theileria sp. and B. caballi, followed by cPCR for 18S rDNA ...
Berglund P, Andonov S, Jansson A, Olsson C, Lundqvist T, Strandberg E, Eriksson S.In equine sports, shoes are used to protect the hooves from wear and tear. In Swedish trotting races, pulling off the shoes to race barefoot is popular because it improves racing time. Good hoof quality is essential for high-performance horses, but not all trotting horses have hooves that tolerate barefoot racing. The ability to race barefoot is a complex trait that is known to be influenced by environmental factors, but the genetic basis of this trait has not been studied. The aim of this study was to estimate genetic parameters and correlations between estimated breeding values for three nov...
Chapard L, Gorssen W, Meyermans R, Hooyberghs K, Buys N, Janssens S.Show jumping is a popular equestrian sport that requires a unique combination of jumping capacity and rideability. It has been shown that genetics play an important role in show jumping performance that has significant implications for horse breeding programmes. This gives an important opportunity for studbooks to breed horses with the potential to perform at the highest level in show jumping competitions. However, show jumping competitions are performed at various levels (from recreational to international level) but only national competition results are used by Warmblood studbooks in most ge...
Santana ML, Franco TGB, Bignardi AB.Barrel racing is a competitive timed rodeo event that challenges horses and riders to complete a cloverleaf pattern around three barrels in the fastest time possible. In this study, we aimed to estimate the genetic parameters of barrel racing time (BRT) and evaluate the most suitable statistical model for its analysis. We compared a repeatability model and three random regression models (RRM) to analyse the longitudinal BRT data in Brazilian Quarter Horses. A total of 356,877 BRT records from 14,108 horses that competed in various events held across Brazil between 2010 and 2024 were analysed. ...
Yokomori T, Tozaki T, Segawa T, Itou T.Previous studies have examined the relationship between hair characteristics and temperament traits in various animals. A partial genetic association has been suggested in humans because whorl formation and neurological development occur simultaneously during the fetal period. In the horse industry, anecdotal evidence suggests a link between the forehead whorl position and temperament. In our previous study, the heritability of forehead whorl positioning was h=0.653, indicating significant genetic contributions in thoroughbreds. Therefore, in this study, we designed a genome-wide association s...
