Horse breeds represent the diverse genetic and phenotypic variations found within the species Equus ferus caballus. These breeds are categorized based on characteristics such as size, conformation, coat color, and temperament, which have been selectively bred over centuries to fulfill specific roles and functions. Common classifications of horse breeds include light horses, draft horses, and ponies, each serving different purposes ranging from riding and racing to work and companionship. This page aggregates peer-reviewed research studies and scholarly articles that explore the genetics, history, and functional attributes of various horse breeds, as well as their impact on equine management and breeding practices.
Choi Y, Jung Y, Wickens CL, Yoon M.Horses are social animals, with early life experiences playing a crucial role in their physiological and behavioral development. This study explored the influence of herd dynamics and foundational training on behavioral and hormonal changes in weaned foals. We examined 13 six-month-old Quarter Horse foals over a three-month training period, performing behavioral observations, temperament assessments, and hormone analyses at the start, midpoint, and end of the training. The results indicated that affiliative behaviors decreased significantly, while agonistic behaviors first increased and then d...
Staiger EA, Pereira de Toledo A, Rizzato Paschoal V, Patterson Rosa L.Horse gaits are a trait highly selected and prized in diverse breeds. Meanwhile, gait classification relies mostly on subjective visual observations by evaluators. Noninvasive equipment able to track locomotion in horses and output quantitative gait parameters is not only helpful in evaluating locomotion but also in designating gait types and its variations. Equine locomotion pattern designation based solely on observer evaluation can be subjective; therefore, utilizing tools that provide quantitative results and track individual limb movements, especially during intermediate-speed gaits, can ...
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...
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...
Gelinder Viklund Å, Blom Y, Eriksson S.The breeding goal of the Swedish Warmblood horse (SWB) is to produce internationally competitive horses in dressage and show jumping. In the current genetic evaluation, breeding values are estimated in multiple-trait animal models where competition performance is the target trait and results from two different young horse tests serve as indicator traits. However, preselection of horses, both for young horse tests and for competitions, is not considered in the current evaluation. The overall aim of this study was to analyse the all-or-none trait start status, in competition and in young horse t...
Ennsmann LH, Licka TF.Most horses are used with horseshoes additionally supported by either dorsoabaxial or dorsal clips. The effects of such clips on bone density and shape of the distal phalanx are currently unclear. The aim of this study was to identify correlations between density and shape of the distal phalanx, comparing front hooves unshod or shod with standard shoes either with two dorsoabaxial clips or with a single dorsal clip. Researchers analyzed Oxspring radiographs of either the left or right front hoof from warmblood horses ( = 137) and ponies ( = 43) aged 3-28 years. The evaluation focused...
Share ER, Mastellar SL, Rumble JN, Eastridge ML.Equine industry housing and feeding management strategies vary widely. Management choices are important as horses spend most of their time in housing environments and demonstrating ingestive/foraging behavior. As of 2023, over 1.4 million Ohioans identified as horse owners and/or enthusiasts. The objectives of this survey were to determine demographics of the Ohio horse industry, commonly used sources of information, knowledge gaps regarding equine management practices, and to explore what may influence equine management choices. Using Qualtrics (Provo, UT), a 52-question online, anonymous sur...
Wang T, Meng J, Peng X, Huang J, Huang Y, Yuan X, Li X, Yang X, Chang X, Zeng Y, Yao X.Yili horses, a versatile breed from Xinjiang, China, are renowned for their racing abilities. However, studies on the links between cardiac morphology, function, and metabolic profiles with performance are limited. This study combined echocardiographic, transcriptomic, and metabolomic analyses to explore these relationships in high-level, average, and untrained Yili horses. Echocardiographic assessments revealed increased left ventricular mass in trained horses, with significant differences in intraventricular septal thickness and left ventricular end-diastolic diameter. RNA sequencing identif...
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...
Knox AL, Fenner K, Zsoldos RR, Wilson B, McGreevy P.The off-the-track Thoroughbred's (OTTTB's) suitability for equestrian retraining and rehoming should always be subject to behavioral considerations. Certain attributes may be advantageous to a horse's racing performance but unfavorable to their prospects off the track. It is important to gain a non-biased understanding of how Thoroughbreds (TBs) in equestrian disciplines compare with other horses behaviorally, to minimize risks of poor welfare and safety outcomes. The current study used owner-reported information ( = 1633) from the Equine Behavior Assessment and Research Questionnaire (E-BARQ)...
Qin X, Xi L, Zhao L, Han J, Qu H, Xu Y, Weng W.Gut microbiota exerts a pivotal function in host nutrient metabolism and maturation of the mucosal immunity. Analyzing the reciprocal interaction between horses and gut microbiota constitutes a crucial aspect of scientific feeding practices. This study aims to investigate the differences in gut microbiota among Hequ horses, Mongolian horses, and Thoroughbred horses, as well as between Thoroughbred horses at two age stages. Unassigned: Paired-end sequencing with a read length of 2×250 bp targeting the V3-V4 region of the 16S rRNA gene in fecal samples was carried out. Subsequently, differences...
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...
Main SC, Ivey JLZ, Strickland LG, Rhinehart JD, Sun X.Land-Grant Institutions and Cooperative Extension Services seek to disseminate information to the public; however, Extension agents differ in areas of expertise, leaving some counties with minimal ability to provide 4-H horse project members with sufficient content knowledge while agents in other counties are more well versed in equine-specific areas. Results from the 2021 and 2023 Tennessee regional and 2022 Eastern National 4-H Hippology contests were used to determine areas of knowledge deficiency. Nutrition, tack, selection, health, and breeds were categories identified as areas in which 4...
Walz KR, McCormick ME, Fedorka CE.Breed bias exists within many of the top disciplines of equestrian sport. Therefore, the objective of this study was to evaluate the influence of breed on performance at the CCI5*-L level of eventing. To do so, the results of all CCI5*-L events from 2014 to 2024 were assessed. Initially, Thoroughbreds were compared to all non-Thoroughbreds, and this was followed by assessing the ten primary breeds. Data included penalties accrued in dressage, cross country, show jumping, and overall. Additionally, the likelihood of completing each phase was assessed. It was found that Thoroughbreds accrued mor...
Coelho C, Vintem C, Silva AS, Santos C, Santos AM, Leite A, Souza V, Siqueira R, Filho HCM, Simões J.The present work aimed to evaluate the influence of a training programme on energy expenditure (EE), cost of transport (COT, cardiac beats to move the body mass during exercise) and metabolic power (Pmet) in young Purebred Lusitano horses used in dressage. With this purpose, nine male horses, ~4 years old, were evaluated before (M1) and after 6 weeks (M2) of a training programme that included 40-80 min of preparatory dressage exercises, 6×/week, individually adjusted. In M1 and M2, the animals were examined in a dressage field test (DFT), when heart rate (HR) and respiratory rate (RR), body...
Everts RE, Caron R, Foster G, McLoone K, Martin K, Brooks SA, Lafayette C.The 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 to no white hairs. Previous studies mapped the locus for roan to the KIT region and observed linked variants in a small number of breeds. However, utilizing those linked markers to determine the roan genotype in other breeds has seen limited success. In this communication we identify a second roan allele (RN2) which, in conjunction with a previously observed roan allele (RN1) disc...
Parra MT, Ayala MSF.A retrospective study was conducted at the Foal Care Equine Perinatology Center in Colombia from October 2017 to May 2023. The goal was to analyze the most frequent pathologies, as well as assess the sexes, ages, and breeds of the patients, with an emphasis on the perinatal population. Out of 945 clinical histories, 776 pertained to perinatology. Survival rates were calculated, and a descriptive analysis was performed. The overall survival rate for neonates was 73.6%, with females constituting 57% of the neonatal patients. The most prevalent breed among mares and neonates was the Creole Colomb...
Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D, Zhao Y.Speed and endurance are the primary goals in racehorse breeding. The Grassland-Thoroughbred is a newly developed breed in northern China that combines speed, endurance, and environmental adaptability. However, current research on the genetic background of this breed and the genes associated with athletic performance remains limited. We conducted whole-genome resequencing on Mongolian (MG), Thoroughbred (TB), Xilingol (XL), and Grassland-Thoroughbred (CY) horses, generating 3813.74 Gb of clean data after quality control. The number of transitions was significantly higher than that of transversi...
Cravana C, Medica P, Fazio E, Satué K, Brancato G, La Fauci D, Bruschetta G.The hypothalamic-pituitary-adrenal (HPA) axis is a neuroendocrine system involved in the coping response to stressful challenges during exercise stimuli. Exercise represents a significant disruptor of homeostasis, inducing an ACTH-cortisol co-secretion, based on different characteristics of exercise in sport horses. Based on this statement, the aim of this study is to evaluate the circulating adrenocorticotropin and cortisol changes in Standardbred trotters, after training and racing sessions, considering the different age and sex. In particular, the aim is to determine to what extent the leve...
Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D.Copy number variation (CNV) is an important source of genetic variation. However, studies utilizing whole-genome sequencing to investigate CNVs in horse populations and their effects on traits remain relatively limited. This study aims to address the lack of research on the impact of copy number variation (CNV) on racing performance in horse populations, providing new insights for locally bred racing breeds. We analyzed 60 offspring derived from the crossbreeding of Thoroughbred horses and Xilingol horses. These horses were temporarily named "Grassland-Thoroughbred" and were divided into two g...
Asti V, Summer A, Ablondi M, Sartori C, Giontella A, Pilastro V, Mecocci S, Cappelli K, Mancin E, Oian A, Mantovani R, Capomaccio S, Sabbioni A.Horses have undergone extensive natural and artificial selection, shaping the diversity of breeds observed today. Native Italian breeds present unique traits influenced by natural selection, such as adaptation to harsh climates, or hoof strength, but face challenges due to population declines and the reduction of their original breeding purpose. This study focuses on five local Italian breeds: Bardigiano, Haflinger, Maremmano, Murgese, and Italian Heavy Draught Horse, to understand how selection has shaped their populations. A total of 1620 individuals were genotyped with a medium-density SNP ...
Ziadi C, Valera M, Laseca N, Perdomo-González D, Demyda-Peyrás S, de Los Terreros AR, Molina A. By simultaneously integrating both genotyped and non-genotyped animals into genetic evaluation, the single-step genomic BLUP method enhanced the accuracy of genetic assessments. This study aimed to compare the increase in prediction reliability (R) between restricted maximum likelihood (REML) and single-step genomic REML (ssGREML) in the Pura Raza Española (PRE) horse breed. The dataset comprised reproductive records for seven fertility traits from 47,502 females, with a total of 57,316 animals represented in the pedigree. A total of 4009 animals were genotyped using the EQUIGENE 90K SNP ar...
Cantatore F, Marcatili M, Giacchi A, Stephenson R, Withers J.Morel-Lavallée lesions (MLLs) are post-traumatic, closed, degloving injuries observed in humans and cats. Morel-Lavallée lesions have never been reported in horses. An 8-year-old Warmblood gelding used for dressage presented with a large swelling on the craniomedial aspect of the stifle that did not respond to conservative treatment. Ultrasonography revealed a large anechogenic fluid-filled cavity with a well-defined capsule. Standing endoscopic examination revealed separation between the deep crural fascia, vastus medialis muscle and skin. Cytology of the fluid collected demonstrated a lymp...
Aleman M, McCue M, Bellone RR.Fatal anesthesia-induced malignant hyperthermia (MH) and rhabdomyolysis with hyperthermia documented in Quarter Horses (QH) breeds are caused by a missense variant in the ryanodine receptor 1 gene (RYR1: XP_023505430.1.:p.(R2454G), designated as MH). The reported cases to date have all been heterozygous, and the allele frequency is suspected to be low. Objective: To determine an accurate estimate of MH allele frequency in multiple horse breeds and investigate whether homozygous animals exist in the population. Methods: In total, 159 227 horses from 16 breeds who were either submitted for cli...
Martinez-Saez L, Marín-García PJ, Llobat ML.Osteochondrosis (OC) is a frequent manifestation of developmental orthopaedic disease, and its severe clinical presentation is known as OC dissecans (OCD). OC is defined as a disruption of the endochondral ossification process in the epiphyseal cartilage, and this disease has been reported in different mammalian species, including humans, dogs, pigs, and horses. OCD is an important cause of lameness in sport horses and is a common cause of impaired orthopaedic potential, whose clinical signs may be of minimal magnitude or manifest as severe joint effusion or clinically noticeable lameness. The...
Ding W, Gong W, Bou T, Shi L, Lin Y, Wu H, Dugarjaviin M, Bai D.Muscle fibers, as the fundamental units of muscle tissue, play a crucial role in determining skeletal muscle function through their growth, development, and composition. To investigate changes in muscle fiber types and their regulatory mechanisms in Mongolian horses (MG), Xilingol horses (XL), and Grassland-Thoroughbreds (CY), we conducted histological and bioinformatic analyses on the gluteus medius muscle of these three horse breeds. Immunofluorescence analysis revealed that Grassland-Thoroughbreds had the highest proportion of fast-twitch muscle fibers at 78.63%, while Mongolian horses had ...
Sigurðardóttir H, Eriksson S, Niazi A, Rhodin M, Albertsdóttir E, Kristjansson T, Lindgren G.Selection for performance in horse breeding benefits from precise genetic insights at a molecular level, but knowledge remains limited. This study used whole-genome sequences of 39 elite and non-elite Icelandic horses to identify candidate causal variants linked to previously identified haplotypes in the STAU2 and RELN genes affecting pace and other gaits. A frameshift variant in linkage disequilibrium with the previously identified haplotypes in the STAU2 gene (r2 = 0.85) was identified within a predicted STAU2 transcript. This variant alters the amino acid sequence and introduces a prema...
Blohina NV, Khrabrova LA.Russia has a significant pedigree diversity of horse breeds with unique gene pools that are well adapted to a wide variety of harsh natural and climatic conditions, are characterized by universal performance and high productive qualities, and are of significant interest to the world horse breeding. Genetic studies of population diversity in horse breeding are very relevant, since many domestic horse breeds are under threat of extinction. Biomaterials (hair, blood, semen) from horses of 15 local breeds bred in the Russian Federation and neighboring countries (CIS) were selected for the research...
Obradovic NA, McFadden A, Martin K, Vierra M, McLoone K, Martin E, Thomas A, Everts RE, Brooks SA, Lafayette C.This paper reports three novel KIT variants likely responsible for previously unexplained white patterning phenotypes observed in three groups of horses. White spots and markings may have substantial consequences on the value and health of domesticated horses. This study aims to elucidate the genetic mechanisms underlying depigmented coat colors to aid in producing prosperous herds. Aligned whole genome sequences were manually screened to identify three polymorphisms in a family of Anglo-Arabian horses (N = 7), a family of Warmblood horses (N = 5), and a single stock-type mare with unexplained...
Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S.Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected...
Science (New York, N.Y.)May 9, 2018
Volume 360, Issue 6396 eaar7711 doi: 10.1126/science.aar7711
de Barros Damgaard P, Martiniano R, Kamm J, Moreno-Mayar JV, Kroonen G, Peyrot M, Barjamovic G, Rasmussen S, Zacho C, Baimukhanov N, Zaibert V....The Yamnaya expansions from the western steppe into Europe and Asia during the Early Bronze Age (~3000 BCE) are believed to have brought with them Indo-European languages and possibly horse husbandry. We analyzed 74 ancient whole-genome sequences from across Inner Asia and Anatolia and show that the Botai people associated with the earliest horse husbandry derived from a hunter-gatherer population deeply diverged from the Yamnaya. Our results also suggest distinct migrations bringing West Eurasian ancestry into South Asia before and after, but not at the time of, Yamnaya culture. We find no ev...
da Silveira JC, Veeramachaneni DN, Winger QA, Carnevale EM, Bouma GJ.Proper cell communication within the ovarian follicle is critical for the growth and maturation of a healthy oocyte that can be fertilized and develop into an embryo. Cell communication within the follicle involves many signaling molecules and is affected by maternal age. Recent studies indicate that cell communication can be mediated through secretion and uptake of small membrane-enclosed vesicles. The goals of this study were to 1) identify cell-secreted vesicles (microvesicles and exosomes) containing miRNAs and proteins within ovarian follicular fluid and 2) determine if miRNA level differ...
Makvandi-Nejad S, Hoffman GE, Allen JJ, Chu E, Gu E, Chandler AM, Loredo AI, Bellone RR, Mezey JG, Brooks SA, Sutter NB.Horse body size varies greatly due to intense selection within each breed. American Miniatures are less than one meter tall at the withers while Shires and Percherons can exceed two meters. The genetic basis for this variation is not known. We hypothesize that the breed population structure of the horse should simplify efforts to identify genes controlling size. In support of this, here we show with genome-wide association scans (GWAS) that genetic variation at just four loci can explain the great majority of horse size variation. Unlike humans, which are naturally reproducing and possess many...
Achilli A, Olivieri A, Soares P, Lancioni H, Hooshiar Kashani B, Perego UA, Nergadze SG, Carossa V, Santagostino M, Capomaccio S, Felicetti M....Archaeological and genetic evidence concerning the time and mode of wild horse (Equus ferus) domestication is still debated. High levels of genetic diversity in horse mtDNA have been detected when analyzing the control region; recurrent mutations, however, tend to blur the structure of the phylogenetic tree. Here, we brought the horse mtDNA phylogeny to the highest level of molecular resolution by analyzing 83 mitochondrial genomes from modern horses across Asia, Europe, the Middle East, and the Americas. Our data reveal 18 major haplogroups (A-R) with radiation times that are mostly confined ...
Petersen JL, Mickelson JR, Cothran EG, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Distl O....Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F(ST) calculations, parsimony, and dista...
McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM, Distl O, Guérin G, Hasegawa T, Hill EW, Leeb T, Lindgren G, Penedo MC, Røed KH....An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50-100 kb and reached background levels within 1-2 Mb. The extent of LD and the level of inbreeding were highest in the ...
Science (New York, N.Y.)February 22, 2018
Volume 360, Issue 6384 111-114 doi: 10.1126/science.aao3297
Gaunitz C, Fages A, Hanghøj K, Albrechtsen A, Khan N, Schubert M, Seguin-Orlando A, Owens IJ, Felkel S, Bignon-Lau O, de Barros Damgaard P....The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski's horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic ...
Fortier LA, Mohammed HO, Lust G, Nixon AJ.Composites of chondrocytes and polymerised fibrin were supplemented with insulin-like growth factor-I (IGF-I) during the arthroscopic repair of full-thickness cartilage defects in a model of extensive loss of cartilage in horses. Repairs facilitated with IGF-I and chondrocyte-fibrin composites, or control defects treated with chondrocyte-fibrin composites alone, were compared before death by the clinical appearance and repeated analysis of synovial fluid, and at termination eight months after surgery by tissue morphology, collagen typing, and biochemical assays. The structure of cartilage was ...
Science (New York, N.Y.)February 13, 2001
Volume 291, Issue 5503 474-477 doi: 10.1126/science.291.5503.474
Vilà C, Leonard JA, Gotherstrom A, Marklund S, Sandberg K, Liden K, Wayne RK, Ellegren H.Domestication entails control of wild species and is generally regarded as a complex process confined to a restricted area and culture. Previous DNA sequence analyses of several domestic species have suggested only a limited number of origination events. We analyzed mitochondrial DNA (mtDNA) control region sequences of 191 domestic horses and found a high diversity of matrilines. Sequence analysis of equids from archaeological sites and late Pleistocene deposits showed that this diversity was not due to an accelerated mutation rate or an ancient domestication event. Consequently, high mtDNA se...
Rieder S, Taourit S, Mariat D, Langlois B, Guérin G.Coat color genetics, when successfully adapted and applied to different mammalian species, provides a good demonstration of the powerful concept of comparative genetics. Using cross-species techniques, we have cloned, sequenced, and characterized equine melanocortin-1-receptor (MC1R) and agouti-signaling-protein (ASIP), and completed a partial sequence of tyrosinase-related protein 1 (TYRP1). The coding sequences and parts of the flanking regions of those genes were systematically analyzed in 40 horses and mutations typed in a total of 120 horses. Our panel represented 22 different horse breed...
Fages A, Hanghøj K, Khan N, Gaunitz C, Seguin-Orlando A, Leonardi M, McCrory Constantz C, Gamba C, Al-Rasheid KAS, Albizuri S, Alfarhan AH....Horse domestication revolutionized warfare and accelerated travel, trade, and the geographic expansion of languages. Here, we present the largest DNA time series for a non-human organism to date, including genome-scale data from 149 ancient animals and 129 ancient genomes (≥1-fold coverage), 87 of which are new. This extensive dataset allows us to assess the modern legacy of past equestrian civilizations. We find that two extinct horse lineages existed during early domestication, one at the far western (Iberia) and the other at the far eastern range (Siberia) of Eurasia. None of these contr...
Ludwig A, Pruvost M, Reissmann M, Benecke N, Brockmann GA, Castaños P, Cieslak M, Lippold S, Llorente L, Malaspinas AS, Slatkin M, Hofreiter M.The transformation of wild animals into domestic ones available for human nutrition was a key prerequisite for modern human societies. However, no other domestic species has had such a substantial impact on the warfare, transportation, and communication capabilities of human societies as the horse. Here, we show that the analysis of ancient DNA targeting nuclear genes responsible for coat coloration allows us to shed light on the timing and place of horse domestication. We conclude that it is unlikely that horse domestication substantially predates the occurrence of coat color variation, which...
Xu X, Arnason U.The sequence of the mitochondrial (mt) DNA of the horse (Equus caballus) was determined. The length of the sequence presented is 16,660 bp. This figure, however, is not absolute due to pronounced heteroplasmy caused by variable numbers of the motif GTGCACCT in the control region of different molecules. Boundaries of the 13 peptide-coding genes were determined by the presence of start and stop codons, and by analogy with other eutherian mtDNAs. Three genes (COIII, NADH3 and NADH4) were not terminated by a stop codon. Comparison among the peptide-coding genes of the horse and eight other mammals...
Science (New York, N.Y.)April 30, 2017
Volume 356, Issue 6336 442-445 doi: 10.1126/science.aam5298
Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK....The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genomes of 14 early domestic horses from the Bronze and Iron Ages, dating to between ~4.1 and 2.3 thousand years before present. We find early domestication selection patterns supporting the neural crest hypothesis, which provides a unified developmental origin for common domestic traits. Within the past 2.3 thousand years, horses lost genetic diversity and archaic DNA tracts introgressed from a now-extinct lineage. They accumulated deleterious mutations later than expected ...
Kalbfleisch TS, Rice ES, DePriest MS, Walenz BP, Hestand MS, Vermeesch JR, O Connell BL, Fiddes IT, Vershinina AO, Saremi NF, Petersen JL, Finno CJ....Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference genome assemblies in terms of contiguity and composition. EquCab2, a reference genome for the domestic horse, was released in 2007. Although of equal or better quality compared to other first-generation Sanger assemblies, it had many of the shortcomings common to them. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, lon...
Bellone RR, Brooks SA, Sandmeyer L, Murphy BA, Forsyth G, Archer S, Bailey E, Grahn B.The appaloosa coat spotting pattern in horses is caused by a single incomplete dominant gene (LP). Homozygosity for LP (LP/LP) is directly associated with congenital stationary night blindness (CSNB) in Appaloosa horses. LP maps to a 6-cM region on ECA1. We investigated the relative expression of two functional candidate genes located in this LP candidate region (TRPM1 and OCA2), as well as three other linked loci (TJP1, MTMR10, and OTUD7A) by quantitative real-time RT-PCR. No large differences were found for expression levels of TJP1, MTMR10, OTUD7A, and OCA2. However, TRPM1 (Transient Recept...
Marklund L, Moller MJ, Sandberg K, Andersson L.The melanocyte-stimulating hormone receptor gene (MC1R) is the major candidate gene for the chestnut coat color in horses since it is assumed to be controlled by an allele at the extension locus. MC1R sequences were PCR amplified from chestnut (e/e) and non-chestnut (E/-) horses. A single-strand conformation polymorphism was found that showed a complete association to the chestnut coat color among 144 horses representing 12 breeds. Sequence analysis revealed a single missense mutation (83Ser-->Phe) in the MC1R allele associated with the chestnut color. The substitution occurs in the second ...
Tetens J, Widmann P, Kühn C, Thaller G.A genome-wide association scan for loci affecting withers height was conducted in 782 German Warmblood stallions, which were genotyped using the Illumina EquineSNP50 Bead Chip. A principal components approach was applied to correct for population structure. The analysis revealed a single major QTL on ECA3 explaining ~18 per cent of the phenotypic variance, which is in concordance with recent reports from other horse populations. The LCORL/NCAPG locus represents a strong candidate gene for this QTL. This locus is among a small number that have consistently been identified to influence human hei...
Leroy G, Mary-Huard T, Verrier E, Danvy S, Charvolin E, Danchin-Burge C.Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate. Results: Depending on breed and method, effective population sizes ranged from 15 to 133 ...
Baumber J, Ball BA, Gravance CG, Medina V, Davies-Morel MC.The objective of this study was to examine the influence of reactive oxygen species (ROS), generated through the use of the xanthine (X)-xanthine oxidase (XO) system, on equine sperm motility, viability, acrosomal integrity, mitochondrial membrane potential, and membrane lipid peroxidation. Equine spermatozoa were separated from seminal plasma on a discontinuous Percoll gradient, and spermatozoa were incubated with 0.6 mM X and 0.05 U/mL XO for 30 minutes. Catalase (150 U/mL), superoxide dismutase (SOD, 150 U/mL), or glutathione (GSH, 1.5 mM) were evaluated for their ability to preserve sperm ...
Hill EW, Gu J, Eivers SS, Fonseca RG, McGivney BA, Govindarajan P, Orr N, Katz LM, MacHugh DE.Variants of the MSTN gene encoding myostatin are associated with muscle hypertrophy phenotypes in a range of mammalian species, most notably cattle, dogs, mice, and humans. Using a sample of registered Thoroughbred horses (n = 148), we have identified a novel MSTN sequence polymorphism that is strongly associated (g.66493737C>T, P = 4.85x10(-8)) with best race distance among elite racehorses (n = 79). This observation was independently validated (P = 1.91x10(-6)) in a resampled group of Thoroughbreds (n = 62) and in a cohort of Thoroughbreds (n = 37, P = 0.0047) produced by the same trainer...
Lindgren G, Backström N, Swinburne J, Hellborg L, Einarsson A, Sandberg K, Cothran G, Vilà C, Binns M, Ellegren H.Genetic studies using mitochondrial DNA (mtDNA) have identified extensive matrilinear diversity among domestic horses. Here, we show that this high degree of polymorphism is not matched by a corresponding patrilinear diversity of the male-specific Y chromosome. In fact, a screening for single-nucleotide polymorphisms (SNPs) in 14.3 kb of noncoding Y chromosome sequence among 52 male horses of 15 different breeds did not identify a single segregation site. These observations are consistent with a strong sex-bias in the domestication process, with few stallions contributing genetically to the do...
Gu J, Orr N, Park SD, Katz LM, Sulimova G, MacHugh DE, Hill EW.Thoroughbred horses have been selected for exceptional racing performance resulting in system-wide structural and functional adaptations contributing to elite athletic phenotypes. Because selection has been recent and intense in a closed population that stems from a small number of founder animals Thoroughbreds represent a unique population within which to identify genomic contributions to exercise-related traits. Employing a population genetics-based hitchhiking mapping approach we performed a genome scan using 394 autosomal and X chromosome microsatellite loci and identified positively selec...
Cieslak M, Pruvost M, Benecke N, Hofreiter M, Morales A, Reissmann M, Ludwig A.Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population r...
Vidal MA, Kilroy GE, Johnson JR, Lopez MJ, Moore RM, Gimble JM.To characterize equine bone marrow (BM)-derived mesenchymal stem cell (MSC) growth characteristics and frequency as well as their adipogenic and osteogenic differentiation potential. Methods: In vitro experimental study. Methods: Foals (n=3, age range, 17-51 days) and young horses (n=5, age range, 9 months to 5 years). Methods: Equine MSCs were harvested and isolated from sternal BM aspirates and grown up to passage 10 to determine cell-doubling (CD) characteristics. Limit dilution assays were performed on primary and passaged MSCs to determine the frequency of colony-forming units with a fibr...
Hill EW, McGivney BA, Gu J, Whiston R, Machugh DE.Thoroughbred horses have been selected for traits contributing to speed and stamina for centuries. It is widely recognized that inherited variation in physical and physiological characteristics is responsible for variation in individual aptitude for race distance, and that muscle phenotypes in particular are important. Results: A genome-wide SNP-association study for optimum racing distance was performed using the EquineSNP50 Bead Chip genotyping array in a cohort of n = 118 elite Thoroughbred racehorses divergent for race distance aptitude. In a cohort-based association test we evaluated geno...
Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK, Brem G, Brooks SA, Distl O, Fries R, Finno CJ, Gerber V, Haase B, Jagannathan V....To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array. Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, ...
Lippold S, Matzke NJ, Reissmann M, Hofreiter M.DNA target enrichment by micro-array capture combined with high throughput sequencing technologies provides the possibility to obtain large amounts of sequence data (e.g. whole mitochondrial DNA genomes) from multiple individuals at relatively low costs. Previously, whole mitochondrial genome data for domestic horses (Equus caballus) were limited to only a few specimens and only short parts of the mtDNA genome (especially the hypervariable region) were investigated for larger sample sets. Results: In this study we investigated whole mitochondrial genomes of 59 domestic horses from 44 breeds an...
Johnson L, Thompson DL, Varner DD.Testicular function is under the control of expression and repression of several genes and gene products, and many of these works through Sertoli cells. The capability of Sertoli cells to regulate spermatogenesis is dependent on Sertoli cell functions and Sertoli cell number. Sertoli cell number has long been thought to be stable in adults with no proliferation of Sertoli cells once adult numbers have been reached. However, adult horses do not have stable Sertoli cell numbers, and new studies indicate that adult Sertoli cells can be made to re-enter mitotic phase under certain experimental con...
