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Topic:Horse Breeds
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.
Detecting SNP markers discriminating horse breeds by deep learning. The assignment of an individual to the true population of origin using a low-panel of discriminant SNP markers is one of the most important applications of genomic data for practical use. The aim of this study was to evaluate the potential of different Artificial Neural Networks (ANNs) approaches consisting Deep Neural Networks (DNN), Garson and Olden methods for feature selection of informative SNP markers from high-throughput genotyping data, that would be able to trace the true breed of unknown samples. The total of 795 animals from 37 breeds, genotyped by using the Illumina SNP 50k Bead ch...
High-Resolution Genotyping of Expressed Equine MHC Reveals a Highly Complex MHC Structure. The Major Histocompatibility Complex (MHC) genes play a key role in a number of biological processes, most notably in immunological responses. The MHCI and MHCII genes incorporate a complex set of highly polymorphic and polygenic series of genes, which, due to the technical limitations of previously available technologies, have only been partially characterized in non-model but economically important species such as the horse. The advent of high-throughput sequencing platforms has provided new opportunities to develop methods to generate high-resolution sequencing data on a large scale and app...
Evaluation of parentage testing using single nucleotide polymorphism markers for draft horses in Japan. We evaluated the utility of single nucleotide polymorphism (SNP) markers for parentage testing in Breton (BR) and Percheron (PR) horses in Japan using the proposed International Society for Animal Genetics (P-ISAG) 147 SNP panel and 414 autosomal SNPs. Genomic DNA was extracted from 98 horses of two breeds, BR (n = 47) and PR (n = 51), and sequenced using next-generation sequencing. The average minor allele frequencies for the P-ISAG panel for BR and PR were 0.306 and 0.301, respectively. The combined probabilities of exclusion (PEs) given two parents and one offspring: exclude a relat...
Clinical effects of a combination of phenylbutazone and omeprazole on chronic lameness in Mongolian horses. Phenylbutazone (PBZ) is the most commonly used drug to treat symptoms of lameness in horses; however, it is associated with adverse effects such as gastric ulcer syndrome (EGUS). Interestingly, many practitioners prescribe omeprazole (OME) concurrently with PBZ to prevent the development of EGUS. However, the efficacy and safety of this practice in Mongolian horses with chronic lameness remain unknown. Objective: To evaluate the clinical effects of a combination of PBZ and OME on chronic lameness in Mongolian horses. Methods: Randomised block experimental design. Methods: Eighteen Mongolian ho...
Genetic Diversity and Maternal Phylogenetic Relationships among Populations and Strains of Arabian Show Horses. Genetic diversity and phylogenetic relationships within the Arabian show horse populations are of particular interest to breeders worldwide. Using the complete mitochondrial DNA D-loop sequence (916 pb), this study aimed (i) to understand the genetic relationship between three populations, the Desert-Bred (DB), a subset of the Kingdom of Saudi Arabia (KSA), United Arab Emirates (UAE) and Bahrain (BAH), the Straight Egyptian (EG) and the Polish bloodline (PL), and (ii) to assess the accuracy of the traditional strain classification system based on maternal lines, as stated by the Bedouin cultur...
Racing Performance of the Quarter Horse: Genetic Parameters, Trends and Correlation for Earnings, Best Time and Time Class. The aim of this study was to evaluate the sprint racing performance of Quarter Horses in Brazil. Estimating genetic parameters, trends and correlations were obtained by single- and two-trait analyses using Bayesian inference (earnings to 2 years of equestrian age, best time and time class at distances of 301 m and 402 m). The data comprised a period of 38 equestrian years (1978 to 2015) with 23,482 sprint race records from 5861 animals. The heritability estimates were of low to moderate magnitude, ranging from 0.10 to 0.37 (single-trait) and from 0.15 to 0.41 (two-traits), and the repeatabilit...
Prevalence and risk factors for laminitis within the Norwegian pony breed Nordlandshest/Lyngshest. Laminitis is a systemic condition resulting in debilitating pain and structural changes within the feet, and hence has major welfare implications. Causes include endocrine and systemic inflammatory conditions. Ponies are frequently affected, and observations in the field suggest that occurrence of laminitis is also common in Norwegian breeds. The aim of this study was to estimate the prevalence and risk factors for laminitis within the Norwegian pony breed Nordlandshest/Lyngshest. Results: The study was a cross-sectional study based on questionnaires sent to members of the Norwegian Nordlands...
Imputed genomes of historical horses provide insights into modern breeding. Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski's horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with high...
Preliminary study of heart rate variability in Criollo horses for the elucidation of their neurophysiological characteristics of autonomic nerve function. The Criollo is an Argentine horse breed with a calm temperament. Although its temperament is considered to be related to its neurophysiological characteristics, the details of this are unknown. Therefore, we analyzed the heart rate variability in Criollos as a preliminary study to deepen the neurophysiological understanding of their autonomic function. Electrocardiograms were recorded from Criollos and Thoroughbreds, and the power spectrum of heart rate variability was analyzed. Compared with Thoroughbreds, Criollos showed (i) a significantly higher high-frequency component, which is an index ...
Genetic diversity and signatures of selection in four indigenous horse breeds of Iran. Indigenous Iranian horse breeds were evolutionarily affected by natural and artificial selection in distinct phylogeographic clades, which shaped their genomes in several unique ways. The aims of this study were to evaluate the genetic diversity and genomewide selection signatures in four indigenous Iranian horse breeds. We evaluated 169 horses from Caspian (n = 21), Turkmen (n = 29), Kurdish (n = 67), and Persian Arabian (n = 52) populations, using genomewide genotyping data. The contemporary effective population sizes were 59, 98, 102, and 113 for Turkmen, Caspian, Persian Ar...
Long-read sequencing assays designed to detect potential gene editing events in the myostatin gene revealed distinct haplotype signatures in the Thoroughbred horse population. We present here the use of targeted, long-read sequencing of the myostatin (MSTN) gene as a model to detect potential gene editing events in Thoroughbred horses. MSTN is a negative regulator of muscle development, making the gene a prime candidate target for gene doping. By sequencing the complete gene in one PCR product, we can catalogue all mutations without the need to produce short-fragment libraries. A panel of reference material fragments with defined mutations was constructed and successfully sequenced by both Oxford Nanopore and Illumina-based methods, showing that gene doping editing ...
Ancient segmentally duplicated LCORL retrocopies in equids. LINE-1 is an active transposable element encoding proteins capable of inserting host gene retrocopies, resulting in retro-copy number variants (retroCNVs) between individuals. Here, we performed retroCNV discovery using 86 equids and identified 437 retrocopy insertions. Only 5 retroCNVs were shared between horses and other equids, indicating that the majority of retroCNVs inserted after the species diverged. A large number (17-35 copies) of segmentally duplicated Ligand Dependent Nuclear Receptor Corepressor Like (LCORL) retrocopies were present in all equids but absent from other extant peris...
In Vitro Transdifferentiation Potential of Equine Mesenchymal Stem Cells into Schwann-Like Cells. Schwann cells (SCs) are essential for the regenerative processes of peripheral nerve injuries. However, their use in cell therapy is limited. In this context, several studies have demonstrated the ability of mesenchymal stem cells (MSCs) to transdifferentiate into Schwann-like cells (SLCs) using chemical protocols or co-culture with SCs. Here, we describe for the first time the in vitro transdifferentiation potential of MSCs derived from equine adipose tissue (AT) and equine bone marrow (BM) into SLCs using a practical method. In this study, the facial nerve of a horse was collected, cut into ...
Genomic inbreeding estimation, runs of homozygosity, and heterozygosity-enriched regions uncover signals of selection in the Quarter Horse racing line. With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (F ), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, a...
Refining the evolutionary tree of the horse Y chromosome. The Y chromosome carries information about the demography of paternal lineages, and thus, can prove invaluable for retracing both the evolutionary trajectory of wild animals and the breeding history of domesticates. In horses, the Y chromosome shows a limited, but highly informative, sequence diversity, supporting the increasing breeding influence of Oriental lineages during the last 1500 years. Here, we augment the primary horse Y-phylogeny, which is currently mainly based on modern horse breeds of economic interest, with haplotypes (HT) segregating in remote horse populations around the wor...
New genomic insights into the conformation of Lipizzan horses. Conformation traits are important selection criteria in equine breeding, as they describe the exterior aspects of the horse (height, joint angles, shape). However, the genetic architecture of conformation is not well understood, as data of these traits mainly consist of subjective evaluation scores. Here, we performed genome-wide association studies on two-dimensional shape data of Lipizzan horses. Based on this data, we identified significant quantitative trait loci (QTL) associated with cresty neck on equine chromosome (ECA)16 within the MAGI1 gene, and with type, hereby differentiating heav...
In Vitro-Produced Equine Blastocysts Exhibit Greater Dispersal and Intermingling of Inner Cell Mass Cells than In Vivo Embryos. In vitro production (IVP) of equine embryos is increasingly popular in clinical practice but suffers from higher incidences of early embryonic loss and monozygotic twin development than transfer of in vivo derived (IVD) embryos. Early embryo development is classically characterized by two cell fate decisions: (1) first, trophectoderm (TE) cells differentiate from inner cell mass (ICM); (2) second, the ICM segregates into epiblast (EPI) and primitive endoderm (PE). This study examined the influence of embryo type (IVD versus IVP), developmental stage or speed, and culture environment (in vitro ...
Genome-Wide Assessment of Runs of Homozygosity by Whole-Genome Sequencing in Diverse Horse Breeds Worldwide. In the genomes of diploid organisms, runs of homozygosity (ROH), consecutive segments of homozygosity, are extended. ROH can be applied to evaluate the inbreeding situation of individuals without pedigree data and to detect selective signatures via ROH islands. We sequenced and analyzed data derived from the whole-genome sequencing of 97 horses, investigated the distribution of genome-wide ROH patterns, and calculated ROH-based inbreeding coefficients for 16 representative horse varieties from around the world. Our findings indicated that both ancient and recent inbreeding occurrences had vary...
A method to generate capture baits for targeted sequencing. Hybridization capture approaches allow targeted high-throughput sequencing analysis at reduced costs compared to shotgun sequencing. Hybridization capture is particularly useful in analyses of genomic data from ancient, environmental, and forensic samples, where target content is low, DNA is fragmented and multiplex PCR or other targeted approaches often fail. Here, we describe a DNA bait synthesis approach for hybridization capture that we call Circular Nucleic acid Enrichment Reagent, or CNER (pronounced 'snare'). The CNER method uses rolling-circle amplification followed by restriction dige...
Genetic variation and domestication of horses revealed by 10 chromosome-level genomes and whole-genome resequencing. Understanding the genetic variations of the horse (Equus caballus) genome will improve breeding conservation and welfare. However, genetic variations in long segments, such as structural variants (SVs), remain understudied. We de novo assembled 10 chromosome-level three-dimensional horse genomes, each representing a distinct breed, and analysed horse SVs using a multi-assembly approach. Our findings suggest that SVs with the accumulation of mammalian-wide interspersed repeats related to long interspersed nuclear elements might be a horse-specific mechanism to modulate genome-wide gene regulato...
Genetic improvement of speed across distance categories in thoroughbred racehorses in Great Britain. Several studies over recent decades have reported a lack of contemporary improvement in thoroughbred racehorse speed, despite apparent additive genetic variance and putatively strong selection. More recently, it has been shown that some phenotypic improvement is ongoing, but rates are low in general and particularly so over longer distances. Here we used pedigree-based analysis of 692,534 records from 76,960 animals to determine whether these phenotypic trends are underpinned by genetic selection responses, and to evaluate the potential for more rapid improvement. We show that thoroughbred spe...
Effect of testicular degeneration on expression of sperm protein at 22 kDa in stallions. Sperm protein at 22 kDa has been associated with fertility. Objective: The objectives of this study were to determine (1) the localization pattern of SP22 on ejaculated and caudal epididymal equine spermatozoa and in epididymal fluid, and to (2) characterize SP22 protein and mRNA expression in testicular and epididymal tissues in response to heat-induced testicular degeneration. Methods: Semen was collected before and after hemi-castration, as well as prior to and following insulation of the remaining testes, and tissue specimens were collected for analysis. Results: Histopathology confirmed ...
Racing performance of juvenile Thoroughbreds with femoropatellar osteochondrosis at auction: A retrospective case-control study. Osteochondrosis dissecans (OCD) is common in the femoropatellar joint in Thoroughbred yearlings for sale at auction and there is no consensus on the effect on racing outcomes. Objective: Describe femoropatellar OCD in juvenile Thoroughbreds and compare the racing performance of affected Thoroughbred horses to siblings and unaffected horses from the same sale. Methods: Retrospective case-control study of juvenile horses born 2010-2016. Methods: Radiographic reports from 27 Thoroughbred auctions of weanling (5-11 months of age) and yearling (12-22 months of age) horses were reviewed to ident...
Genomic association using principal components of morphometric traits in horses: identification of genes related to bone growth. The measurement of morphometric traits in horses is important for determining breed qualification and is one of the main selection criteria for the species. The development of an index (HPC) that consists of principal components weighted by additive genetic values allows to explore the most relevant relationships using a reduced number of variables that explain the greatest amount of variation in the data. Genome-wide association studies (GWAS) using HPC are a relatively new approach that permits to identify regions related to a set of traits. The aim of this study was to perform GWAS using HP...
5’UTR Variant in KIT Associated With White Spotting in Horses. Mutations in KIT, a gene that influences melanoblast migration and pigmentation, often result in mammalian white spotting. As of February 2023, over 30 KIT variants associated with white spotting were documented in Equus caballus (horse). Here we report an association of increased white spotting on the skin and coat with a variant in the 5'UTR of KIT (rs1149701677: g.79,618,649A>C). Horses possessing at least one alternate allele demonstrate phenotypic characteristics similar to other KIT mutations: clear borders around unpigmented regions on the body, face, and limbs. Using a quantitative ...
Identification and characterization of single nucleotide polymorphisms in DMRT3 gene in Indian horse (Equus caballus) and donkey (Equus asinus) populations. Equines' ability in racing and riding as well as gaitedness have influenced the human civilization. Aim of this study was to identify and characterize the novel polymorphisms or SNPs in gene in Indian horse and donkey breeds. In this study, the gene was sequenced and characterized in 72 Indian horses' and 33 Indian donkeys' samples. One SNP (A > C) at 878 was found in studied horses while identical SNPs (A > C) at two different nucleotide positions i.e., 878 and 942 in gene (chromosome 23) were observed in studied Indian donkey breeds. Horses and donkeys both have a non-synony...
Evaluation of an HMGA2 variant contribution to height and basal insulin concentrations in ponies. The HMGA2:c.83G>A variant was identified in Welsh ponies having pleiotropic effects on height and insulin concentration. Objective: Determine whether the HMGA2:c.83G>A variant is associated with decreased height and higher basal insulin concentrations across pony breeds. Methods: Two hundred thirty-six ponies across 6 breeds. Methods: Cross-sectional study. Ponies were genotyped for the HMGA2:c.83G>A variant and phenotyped for height and basal insulin concentrations. Stepwise regression was performed for model analysis using a linear regression model for height and mixed linear model ...
Comparison of muscle metabolomics between two Chinese horse breeds. With their enormous muscle mass and athletic ability, horses are well-positioned as model organisms for understanding muscle metabolism. There are two different types of horse breeds-Guanzhong (GZ) horses, an athletic breed with a larger body height (~148.7 cm), and the Ningqiang pony (NQ) horses, a lower height breed generally used for ornamental purposes-both inhabited in the same region of China with obvious differences in muscle content. The main objective of this study was to evaluate the breed-specific mechanisms controlling muscle metabolism. In this study, we observed muscle glycogen, ...
Genome-wide single-nucleotide polymorphism data and mitochondrial hypervariable region 1 nucleotide sequence reveal the origin of the Akhal-Teke horse. The study investigated the origin of the Akhal-Teke horse using genome-wide single-nucleotide polymorphism (SNP) data and mitochondrial hypervariable region 1 (HVR-1) nucleotide sequences. Methods: Genome-wide SNP data from 22 breeds (481 horses) and mitochondrial HVR-1 sequences from 24 breeds (544 sequences) worldwide to examine the origin of the Akhal- Teke horse. The data were analyzed using principal component analysis, linkage disequilibrium analysis, neighbor-joining dendrograms, and ancestry inference to determine the population relationships, ancestral source, genetic structure, and r...
A genome-wide landscape of mRNAs, miRNAs, lncRNAs, and circRNAs of skeletal muscles during dietary restriction in Mongolian horses. The proportion of different muscle fibers is essential for the horse breed's aptitude for athletic activities. Adaptation of locomotor muscle is correlated with altered physiologic conditions. To investigate the adaptive changes of muscle fiber phenotype and transcriptome in horse skeletal muscle during dietary restriction (DR). The muscle fiber type distribution and deep RNA-seq analysis of detecting differentially expressed mRNAs (DEGs), miRNA (DEMIRs), lncRNAs (DELs), circRNAs (DECs), and their function analysis were investigated in gluteus medius muscle of Mongolian horses during DR. A tot...
