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.
Todd EW.Antiproteinase sera were prepared by immunizing horses with filtrates from a selected strain of group A streptococcus. This strain, which produced high titred proteinase but no erythrogenic toxin, was selected from forty-two strains of group A streptococci which produced varying amounts of proteinase. A few strains belonging to groups B, C, and G were also tested; they were all proteinase-negative. Methods are described for titrating streptococcal proteinase in crude culture filtrates and for measuring the antiproteinase activity of serum. The antiproteinase titres of sera from immunized horse...
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...
Jarquín-Díaz VH, Dayaram A, Soilemetzidou ES, Desvars-Larrive A, Bohner J, Buuveibaatar B, Kaczensky P, Walzer C, Greenwood AD, Löber U.The microbial composition of host-associated microbiomes is influenced by co-evolutionary interactions, host genetics, domestication, and the environment. This study investigates the contribution of environmental microbiota from freshwater bodies to the gastrointestinal microbiomes of wild khulans (Equus hemionus hemionus, n = 21) and compares them with those of captive khulans (n = 12) and other equids-Przewalski's horse (n = 82) and domestic horse (n = 26). Using PacBio technology and the LotuS pipeline for 16S rRNA gene sequencing, we analyze microbial diversity and conduct ...
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.
Wang C, Zeng Y, Wang J, Wang T, Li X, Shen Z, Meng J, Yao X.The Yili horse is a riding-type breed that has been continuously bred independently in China. The genetics of body conformation and racing performance traits need to be comprehensively considered in making breeding decisions. This study is the first to estimate the genetic parameters of 13 body conformation and racing performance traits in Yili horses using a linear model. In total, 9937 body conformation and 2576 race records of 9100 Yili horses obtained from 1993 to 2022 were reviewed. The results showed that heritability estimates of body measurement traits were medium to high, ranging from...
Facile V, Magliocca M, Dini FM, Imposimato I, Mariella J, Freccero F, Urbani L, Rinnovati R, Sel E, Gallina L, Castagnetti C, Galuppi R, Battilani M....Equine piroplasmosis is a tick-borne disease caused by and species. Despite its presence in Europe, no laboratory testing is required for animal movement, even though some countries remain free of this disease. Differentiating between species and genotypes is crucial to determine the most effective treatment, as dosage, active compounds, and duration vary. However, diagnosis is often challenging due to genetic variability and the limited sensitivity of molecular methods. The aims of this study were to compare the performances of different molecular diagnostic tests to identify the most effec...
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...
Diekmann I, Krücken J, Kuzmina TA, Bredtmann CM, Louro M, Kharchenko VA, Tzelos T, Matthews JB, Madeira de Carvalho LM, von Samson-Himmelstjerna G.Morphologically, 64 strongylid species have been described in equines. Co-infections are common, with up to 29 species reported in a single horse. Morphological identification of these species is time consuming and requires expert knowledge due to their similar appearance. Therefore, non-invasive identification methods are needed. DNA barcoding offers a rapid and reliable tool for species identification and the discovery of cryptic species for these most common parasitic nematodes of equines. In total, 269 COI and 312 ITS-2 sequences from 27 equine Strongylidae species, including sequences fro...
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 ...
Li X, Wang Z, Zhu M, Wang B, Teng S, Yan J, Wang H, Yuan P, Cao S, Qu X, Wang Z, Zhan K, Choudhury MP, Yang X, Bao Q, He S, Liu L, Zhao P, Jiang J....Horse domestication revolutionizes human civilization by transforming transportation, agriculture, and warfare patterns. Despite extensive studies on modern domestic horse origins, the intricate demographic history and genetic signatures underlying pony size remain unexplored. Here, a high-quality genome assembly of the Chinese Debao pony is presented, and 452 qualified individuals from 64 horse breeds worldwide are extensively analyzed. The authors' results reveal the conservation of ancient components in East Asian horses and close relationships between Asian horses and Western pony lineages...
Yang L, Li P, Huang X, Wang C, Zeng Y, Wang J, Yao X, Meng J.Training is essential for enhancing equine athletic performance, but the genetic mechanisms that regulate athletic performance are unknown. Therefore, this paper aims to identify candidate genes and metabolic pathways for the effects of training on equine athletic performance through multi-omics analyses. Methods: The experiment selected 12 untrained trot-type Yili horses, which underwent a 12-week professional training program. Blood samples were collected at rest before training (BT) and after training (AT). Based on their race performance, whole blood and serum samples from 4 horses were ch...
Ziadi C, Demyda-Peyrás S, Valera M, Perdomo-González D, Laseca N, Rodríguez-Sainz de Los Terreros A, Encina A, Azor P, Molina A.The single-step best linear unbiased predictor (ssGBLUP) has emerged as a reference method for genomic selection in recent years due to its advantages over traditional approaches. Although its application in horses remains limited, ssGBLUP has demonstrated the potential to improve the reliability of estimated breeding values in livestock species. This study aimed to assess the impact of incorporating genomic data using single-step restricted maximum likelihood (ssGREML) on reliability (R) in the Pura Raza Española (PRE) horse breed, compared to traditional pedigree-based REML. Methods: The an...
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...
Du W, Sun Q, Hu S, Yu P, Kan S, Zhang W.Mitochondria are semi-autonomous organelles that play a crucial role in the energy budget of animal cells and are closely related to the locomotor abilities of animals. Equidae is renowned for including two domesticated species with distinct purposes: the endurance-oriented donkey and the power-driven horse, making it an ideal system for studying the relationship between mitochondria and locomotor abilities. In this study, to cover the genetic diversity of donkeys, we sequenced and assembled six new mitochondrial genomes from China. Meanwhile, we downloaded the published mitochondrial genomes ...
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...
Stefaniuk-Szmukier M, Bieniek A, Ropka-Molik K, Bellone RR.Congenital stationary night blindness (CSNB) has been connected to the leopard complex spotting phenotype (LP) in various horse breeds. CSNB associated with LP is thought to be caused by a 1378 bp insertion in TRPM1, with homozygotes being nightblind and having few to no spots of pigment in their white patterned area. This study aimed to assess the prevalence of CSNB alleles in tarant-colored horses in Poland through a three-primer system for an allele-specific Polymerase Chain Reaction (PCR). The TRPM1 gene insertion was genotyped in 221 horses belonging to Małopolska, Felin and Shetland Pon...
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...
Qiu Y, Jiang J, Yi X, Wang S, Sun X.This study investigated the immunoglobulins (IG) gene locus structure and expression diversity in local Chinese horse and donkey breeds, including Ningqiang, Guanzhong horses, and varieties such as Guanzhong, Jiami, and Northern Shaanxi donkey using genome alignment and high-throughput sequencing. The aim was to expand understanding of IG expression patterns in horses, donkeys, and their different breeds. The results revealed that the donkey IGH locus contains 117 VH genes (23 functional), 44 DH genes, and 8 JH genes, arranged in a VH-DH-JH sequence on chromosome 7, spanning approximately 1189...
Frontiers in geneticsFebruary 27, 2025
Volume 16 1534461 doi: 10.3389/fgene.2025.1534461
Barber AM, Kingsley NB, Peng S, Giulotto E, Bellone RR, Finno CJ, Kalbfleisch T, Petersen JL.The Functional Annotation of Animal Genomes (FAANG) consortium aims to annotate animal genomes across species, and work in the horse has substantially contributed to that goal. As part of this initiative, chromatin immunoprecipitation with sequencing (ChIP-seq) was performed to identify histone modifications corresponding to enhancers (H3K4me1), promoters (H3K4me3), activators (H3K27ac), and repressors (H3K27me3) in eight tissues from two Thoroughbred stallions: adipose, parietal cortex, heart, lamina, liver, lung, skeletal muscle, and testis. The average genome coverage of peaks identified by...
Novak BJ, Ryder OA, Houck ML, Walker K, Russell L, Russell B, Walker S, Arenivas SS, Aston L, Veneklasen G, Ivy JA, Koepfli KP, Rusnak A, Simek J....Cloning from historically cryopreserved cells offers a potential means to restore lost genetic variation or increase the representation of particular lineages within bottlenecked species, provided such biobanked materials are archived for such genetic rescue applications. One species for which cloning can provide genetic management benefits is Przewalski's horse, . All ~1800 living Przewalski's horses, distributed across ex situ breeding facilities and in situ reintroduction sites, are descended from one or more of the five founder lineages established by the 12 horses captured from the wild b...
Kelly RF, Galbraith E, Zahid O, Chaundhry U, Sargison N.Grazing animal species kept in zoological collections can be at risk of significant gastrointestinal nematode (GIN) infections. Little work has been undertaken to understand GIN species dynamics within co-grazed hosts. This study aimed to describe the species diversity of GINs found in faeces of grazing animals in a Scottish zoological collection. Methods: At a single time-point, freshly voided faecal samples were collected randomly from horses, sheep, goats, alpacas and deer. Faecal worm egg counts (FWECs) were conducted using a saturated saline centrifugal flotation cuvette technique. The ne...
Finno CJ.Nutrigenomics defines the interaction between the nutrients in our food and the genes in our body. Examples from human medicine of diseases and associated genes include lactose intolerance (genetic variants in LCT lactase), hypercholesteremia (low density lipoprotein receptor, LDLR) and caffeine sensitivity (adenosine A2A receptor, ADORA2A). In horses, examples include Hyperkalemic Periodic Paralysis (HYPP), where clinical signs of disease are managed through maintaining a diet low in potassium and Polysaccharide Storage Myopathy Type 1 (PSSM1), where low starch and high fat diets are recommen...
Han J, Shao H, Sun M, Gao F, Hu Q, Yang G, Jafari H, Li N, Dang R.Genetic diversity in livestock and poultry is critical for adapting production systems to future challenges. However, inadequate management practices, particularly in developing countries, have led to the extinction or near extinction of several species. Understanding the genetic composition and historical background of local breeds is essential for their effective conservation and sustainable use. This study compared the genomes of 30 newly sequenced Ningqiang ponies with those of 56 other ponies and 104 horses to investigate genetic diversity, genetic differentiation, and the genetic basis o...
Uprety T, Swan M, Kennedy L, Bryant U, Cassone L, Loynachan A, Janes J, Evely MM, Calvaruso FC, Quick M, Morgan J, Abdelrazek S, Lahmers K, Carter C....Clostridium piliforme is an obligate intracellular filamentous bacterium that causes Tyzzer disease (TD) in many animals. The disease manifests as severe, multifocal necrotizing hepatitis, with a high fatality rate in foals. Through retrospective investigation, we detected C. piliforme in 43 equine necropsy cases from 2012 to 2024. Positive cases were diagnosed from February to July, peaking in May. The age of affected foals ranged from 4 days to 2 months. Histologically, all cases had necrotizing hepatitis with multifocal, coalescing pinpoint, tan or reddish foci. Since only a partial 16S rRN...
Science (New York, N.Y.)March 28, 2025
Volume 387, Issue 6741 eadr8589 doi: 10.1126/science.adr8589
Castiglione GM, Chen X, Xu Z, Dbouk NH, Bose AA, Carmona-Berrio D, Chi EE, Zhou L, Boronina TN, Cole RN, Wu S, Liu AD, Liu TD, Lu H, Kalbfleisch T....Horses are among nature's greatest athletes, yet the ancestral molecular adaptations fueling their energy demands are poorly understood. Within a clinically important pathway regulating redox and metabolic homeostasis (NRF2/KEAP1), we discovered an ancient mutation-conserved in all extant equids-that increases mitochondrial respiration while decreasing tissue-damaging oxidative stress. This mutation is a de novo premature opal stop codon in KEAP1 that is translationally recoded into a cysteine through previously unknown mechanisms, producing an R15C mutation in KEAP1 that is more sensitive to ...
