Genotyping in horses involves analyzing the genetic makeup of individual horses to identify specific genetic markers. This process aids in understanding genetic variations that may influence traits such as coat color, disease susceptibility, and performance capabilities. Genotyping can be used in breeding programs to select for desirable traits and manage genetic diversity within populations. Common methods for genotyping include single nucleotide polymorphism (SNP) analysis and microsatellite markers. This page compiles peer-reviewed research studies and scholarly articles that explore the methodologies, applications, and implications of genotyping in equine genetics and breeding.
Ryder OA, Sparkes RS, Sparkes MC, Clegg JB.1. Through the use of isoelectric focusing and peptide analysis, the hemoglobins of Przewalski's horse. Equus przewalskii and the domestic horse, E. caballus have been compared. 2. Przewalski's horses have two separate alpha-globin chain polymorphisms similar to domestic horses. Each hemoglobin phenotype could be accurately determined by isoelectric focusing. 3. Confirmation of the electrofocusing hemoglobin determinations was made by comparison to amino acid composition analyses of purified tryptic peptides and by analysis of the rare hemoglobins phenotypes observed in a family of Norwegian t...
The Journal of heredityMay 1, 1978
Volume 69, Issue 3 146-148 doi: 10.1093/oxfordjournals.jhered.a108913
Adalsteinsson S.The coat colors of 161 progeny from matings between 10 yellow dun and 6 blue dun stallions and mares of 8 different colors are described. The results confirm the previous hypothesis that a dominant dilution gene, D, converts bay to yellow dun with dark mane and tail, chestnut to yellow dun and dun mane and tail, and black to blue dun (mouse, grullo). The palomino gene, c cr, on the other hand, is hypostatic to black and blue dun. In heterozygous form, c cr converts bay to buckskin, and chestnut and sorrel to palomino, and results in blue-eyed white when homozygous. No particular effect of D is...
Weitkamp LR.Polymorphism of equine Gc protein was demonstrated by immunofixation electrophoresis with a goat anti-human Gc antibody. Three different phenotypes, F, FS and S, were found. Family data supported the genetic theory of two autosomal codominant alleles, GcF and GcS. Both alleles occurred in Standardbred, Thoroughbred and Arabian horses and in Shetland ponies. A frequency of 0.23 for GcS in the American Standardbred horse indicates the system should be useful for problems of identification and parentage.
Juneja RK, Gahne B, Sandberg K.Horizontal polyacrylamide gel electrophoreses, on 10% separation gel, of horse serum revealed polymorphism of the vitamin D binding protein (Gc protein) and another post-albumin protein (Pa). Family data supported the hypothesis that Gc and Pa types were controlled by autosomal codominant alleles. For both Gc and Pa proteins, the homozygous types showed a single fraction while the heterozygous type had two fractions. Pa types were found to be identical to the post-albumin types reported earlier by starch gel electrophoresis. Two Gc alleles, GcF and GcS, and three Pa alleles, Pa D, Pa F and Pa ...
Stewart F, Allen WR, Moor RM.Rat testicular radioreceptor assays specific for FSH and LH were used to determine the FSH:LH ratio of PMSG produced by horse, donkey, mule and hinny conceptuses. Measurements of FSH and LH activities in PMSG produced both in vivo and in vitro by the four types of conceptuses showed that the genotype of the foetus markedly influences the FSH:LH ratio of PMSG. The FSH:LH ratio of PMSG produced by the horse conceptus was around unity whereas the ratio of PMSG produced by the donkey conceptus was as low as 0-2. Furthermore, the hybrid mule and hinny conceptuses both produced PMSG with an FSH:LH r...
The goal of this research was to evaluate the ability of the genotyping information available in the Brazilian Criollo Horse Stud Book to describe the genetic variability of the breed and the exclusion probability determined in comparative tests. Altogether, two softwares were used in the analyses of the available genotypes: Cervus 3.0.3 and Genepop 4.0. Eight microsatellite markers totaled 109 alleles, with an average of 13.6 +/- 0.6 alleles per locus. Large differences between expected and observed heterozygosity were ubiquitous (0.821 +/- 0.07 and 0.470 +/- 0.17, respectively). Although the...
Feral horses in Theodore Roosevelt National Park (TRNP) represent an iconic era of the North Dakota Badlands. Their uncertain history raises management questions regarding origins, genetic diversity, and long-term genetic viability. Hair samples with follicles were collected from 196 horses in the Park and used to sequence the control region of mitochondrial DNA (mtDNA) and to profile 12 autosomal short tandem repeat (STR) markers. Three mtDNA haplotypes found in the TRNP horses belonged to haplogroups L and B. The control region variation was low with haplotype diversity of 0.5271, nucleotide...
Exertional rhabdomyolysis (ER) and its familial basis in Warmblood horses is incompletely understood. Objective: To describe the case details, clinical signs and management of ER-affected Warmblood horses from a family with a high prevalence of ER, to determine if histopathological signs of polysaccharide storage myopathy (PSSM) and the glycogen synthase (GYS1) mutation are associated with ER in this family, and to investigate potential risk factors for development of ER. Methods: A family consisting of a sire with ER and 71 of his descendants was investigated. History of episodes of ER, husba...
A breed known for its versatility, the American Quarter Horse (QH), is increasingly bred for performance in specific disciplines. The impact of selective breeding on the diversity and structure of the QH breed was evaluated using pedigree analysis and genome-wide SNP data from horses representing 6 performance groups (halter, western pleasure, reining, working cow, cutting, and racing). Genotype data (36 037 single nucleotide polymorphisms [SNPs]) from 36 Thoroughbreds were also evaluated with those from the 132 performing QHs to evaluate the Thoroughbred's influence on QH diversity. Results s...
Qin S, Kulabieke T, Mizhamuhan D, Zhang M, Jin M, Abula G, Pi M, Wang H, Zhang Y, Guo Q.Equine theileriosis, caused by the protozoan parasite , represents a significant economic threat to the equine industry. In Xinjiang, China, an endemic area for this disease, systematic research on the genetic diversity of has been notably lacking. The aim of this study was to obtain molecular epidemiological data pertaining to the parasite in selected regions of Xinjiang, China, and analyze the genetic characteristics (including rRNA, , and genes) and genotype distribution patterns of isolates from these regions, providing a scientific basis for developing targeted prevention and control s...
Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D.Speed is not only the primary objective of racehorse breeding but also a crucial indicator for evaluating racehorse performance. This study investigates a newly developed racehorse breed in China. Through whole-genome resequencing, we selected 60 offspring obtained from the crossbreeding of Thoroughbred horses and Xilingol horses for this study. This breed is tentatively named "Grassland-Thoroughbred", and the samples were divided into two groups based on racing ability: 30 racehorses and 30 non-racehorses. Based on whole-genome sequencing data, the study achieved an average sequencing depth o...
Van Buren SL, Petersen JL, Brown CT, Finno CJ.With advancing genomic technologies, single-nucleotide polymorphism (SNP) arrays and whole genome sequencing (WGS) have become essential tools in equine genetic research. In this study, we assessed the concordance in SNP calls and trait-mapping efficacy by comparing data of 21 horses both genotyped on the Equine 670 K SNP array and sequenced at either ~12× or ~30× depth. Our analysis revealed that higher sequencing depths were significantly associated with fewer discordant calls between platforms. Additionally, we investigated the most frequent no-call and discordant positions and identifi...
Moroudi RS, Mahboudi H, Mahboudi F.The Dareshouri horse breed is one of Iran's native equine breeds, originating from the Dareshouri tribe, a subgroup of the Qashqai nomads. This breed has a history spanning over 500 years. Horses of this breed have smooth nates, tall stature, raised tails and strong skeletal muscles. This is the first study to investigate the effect of genetics on athletic performance in the Dareshouri breed. For this purpose, in this study, the genotype combination of two important variants, including the rs397152648Single nucleotide polymorphism (SNP) and Short interspersed nuclear element (SINE) insertion, ...
Masuda M, Tozaki T, Kawate K, Furukawa R, Kikuchi M, Ishige T, Kakoi H.The Miyako horse is one of the eight Japanese native horse breeds and is scarce in terms of population size. Japanese native horses are believed to be descended from Mongolian horses and represent a precious lineage that has preserved its traits for over a thousand years in Japan. Genetic analysis of the endangered Miyako horse is useful for preserving its original phenotypic traits. This study analysed the genetic variation in trait-related genes for coat colour (), body composition (), gait (), and temperament () in 46 extant Miyako horses. In addition, because numerous Miyako horses have ve...
Błaszczak A, Olczak K, Stefaniuk-Szmukier M, Tomczyk-Wrona I, Musiał AD, Grzegorczyk J, Długosz B, Szmatoła T, Ropka-Molik K.Insect bite hypersensitivity (IBH) is a prevalent allergic skin disease in horses that significantly affects animal welfare and shows evidence of genetic predisposition. Objective: Understanding the genetic basis of IBH can improve management and breeding strategies. The Equine80K BeadChip microarray was used to identify genomic regions associated with the occurrence of IBH in Hucul horses. Methods: Hair samples were collected from 127 Hucul horses, including both affected individuals and controls. DNA was extracted and genotyped. A genome-wide association study (GWAS) was performed to identif...
Ropka-Molik K, Musiał AD, Majtyka A, Bieniek A, Ayad A, Muszyński S, Stefaniuk-Szmukier M.The DMRT3 gene, often referred to as the "gait keeper," plays a key role in controlling alternative gaits in horses, such as tölt and pace. This study aimed to determine the frequency of known and to screen for potential novel polymorphisms within the second exon of the DMRT3 gene. Methods: A total of 244 blood or hair samples were collected from representative individuals of the six horse breeds: gaited (Icelandic Horse, French Trotter), non-gaited (Arabian Horse, Malopolski Horse), and pony breeds (Welsh Pony, Shetland Pony). Methods: The second exon of the DMRT3 gene analyzed using Sanger ...
Mienaltowski MJ, Hernandez S, Nastrini E, Wickens CL, McCue ME, Rosa LP, Norton EM, McCoy AM, Brooks SA.The S1094 United States Department of Agriculture Multistate Research Project is a collaborative effort utilizing equine genetics and genomics to improve horse health and well-being. It also provides educational resources and genetic testing tools to equine industry stakeholders. Objective: A survey assessed the knowledge, priorities, and information sources of U.S. horse owners and enthusiasts regarding equine genetic testing to inform future outreach and research efforts. Methods: An online survey was distributed from March to October 2024, targeting horse owners and enthusiasts across the U...
Crooijmans RPMA, Gonzalez Prendes R, Colli L, Del Corvo M, Barbato M, Somenzi E, Tosser-Klopp G, Meszaros G, Ajmone-Marsan P, Weigend S, Wallner B....Molecular genetic characterization of genetic resources is essential to study biodiversity. Whereas whole genome sequencing is still relatively expensive, low density SNP arrays offer a cost-effective and standardized solution. However, most of the current arrays are species specific. Their high SNP density often exceeds diversity mapping requirements and remains too costly for many genetic resource managers. The IMAGE H2020 project aimed at developing a low-cost multispecies SNP array to facilitate mapping of the genetic diversity in samples stored in gene banks and in vivo (on farm) traditi...
Furukawa R, Tozaki T, Kawate K, Kikuchi M, Ishige T, Fukui E, Kakoi H.A subset of single-nucleotide polymorphisms (SNPs) are associated with various phenotypes, including diseases, coat colour, and athletic performance, and are widely used in medical and veterinary fields. In this study, we developed a novel method for direct SNP genotyping from whole blood without DNA extraction. Thoroughbred blood samples were diluted 100-fold with Milli-Q water and analysed using real-time polymerase chain reaction (PCR) with hydrolysis probes. Specificity and sensitivity were improved by increasing the annealing temperature and number of PCR cycles. Genotyping results for SN...
Gmel AI, Pirani A, McInnis L, Neuditschko M.Single nucleotide polymorphism (SNP) arrays are commonly used in livestock genetics to investigate complex traits including genome-wide associations and fine mapping, genomic prediction and genetic diversity analyses. In a European equine diversity study, we analysed the AxiomTM Equine 670K SNP genotype data from 2,768 equids representing 20 horse breeds and one donkey breed. Using a strict detection setting to identify genome-wide runs of homozygosity (ROH), 169 purebred horses displayed fewer ROH segments than F1 crosses. Under medium and relaxed settings, ROH counts increased, while some ho...
Abdulkadir A, Kabir J, Bello M, Olayinka B.Methicillin resistant Staphylococcus aureus (MRSA) represents a worrying example of antimicrobial resistance, and it is essential to acquire new information to monitor the spread and limit it further diffusion. This study aimed to characterise 22 MRSA isolates from horses, dogs, cats, and their human handlers focusing on spa typing. In the analysis of the sequences obtained, the spa type is "unknown" (unidentified) and all the sequences except one had repeats previously not known in all databases potentially indicating new spa-repeats. This could possibly indicate either permanent import of no...
Kovács M, Hegedűs B, Mihók S, Knop R, Szabó C, Posta J.The conservation of genetic diversity in historically structured horse breeds requires fi-ne-scale population genetic evaluation beyond conventional pedigree-based approaches. The present study assessed genetic diversity, population structure, and mare family differentiation in a Lipizzan horse population using 16 ISAG/FAO-recommended microsatellite markers. A total of 172 mares representing 29 mare families were genotyped. All loci were polymorphic, with a mean number of alleles per locus of 6.69 and a mean effective number of alleles of 3.56. The average polymorphism information content (PIC...
Caceres AM, Sperandio LMS, Alvarenga NACA, Borges AS, Oliveira-Filho JP.Bull-catching (vaquejada) accounting for approximately 13% of sport horses in Brazil. Genetic screening has enabled strategies to reduce the spread of inherited disorders, including Hereditary Equine Regional Dermal Asthenia (HERDA), a major skin disease included in the Six Panel required for registration by the Brazilian Quarter Horse Breeders Association. Although the HERDA-associated variant has been extensively studied in other disciplines, it had not been evaluated in Bull-catching Quarter Horses (QH). Objective: The present study aimed to determine the allele frequency of the pathogenic ...
Maharana BR, Ganguly A, Malik R, Kumar A, Khanna S, Kumar B, Potliya S, Singh H, Dash A, Sahu S.Equine piroplasmosis, caused by Theileria equi, has been widely studied globally, but genetic diversity research in India remains limited. Analysis of 306 horse blood samples revealed T. equi infection in 10.78% by microscopy and 21.24% by PCR. Universal primers targeting 18S rRNA of T. equi and Babesia caballi were used, followed by species-specific primers generating 435 bp amplicons. Sequenced PCR-positive samples revealed high homology (99.52-100% in India, 95.89-100% globally), with all Indian isolates classified as genotype A. The EMA-1 gene phylogenetic analysis confirmed the insights f...
Ibrahim MA, Noshy MM, Mohamed HRH, Abd El-Gawad MEH.This study combined classical cytogenetics and ISSR molecular markers to characterize genetic diversity in 24 Egyptian Arabian horses. Karyotyping revealed the standard equine chromosome number (2n = 64) with no numerical or structural abnormalities. Chromosome measurements were consistent with ISCN Equine standards: autosomal relative lengths (RL%) followed the expected size hierarchy, biarmed chromosomes displayed metacentric to submetacentric morphology (CI = 37-50%), and recalculated centromeric indices confirmed the presence of measurable p-arms on all acrocentric chromosomes. ISSR an...
