Omneity® Pellets
All-In-One Vitamin & Mineral Pellet
Topic:Inbreeding
Inbreeding in horses refers to the mating of individuals that are closely related genetically, resulting in offspring with a higher degree of genetic similarity. This practice can lead to an increased risk of homozygosity for deleterious alleles, which may affect health, performance, and reproductive traits. Inbreeding is often measured by the inbreeding coefficient, which quantifies the probability that two alleles at a locus are identical by descent. While inbreeding can consolidate desirable traits within a breed, it may also reduce genetic diversity and increase the likelihood of inherited disorders. This page compiles peer-reviewed research studies and scholarly articles that explore the genetic, physiological, and health implications of inbreeding in equine populations.
Genomic insights into the genetic diversity, lateral gaits and high-altitude adaptation of Chakouyi (CKY) horses. Chakouyi (CKY) horses from the Qinghai‒Xizang Plateau are well known for their unique lateral gaits and high-altitude adaptation, but genetic mechanisms underlying these phenotypes remain unclear. This study presents a comparison of 60 newly resequenced genomes of gaited CKY horses with 139 public genomes from 19 horse breeds. Population structure analyses (admixture, PCA, and neighbor-joining tree) reveal a close genetic relationship between CKY and other highland breeds (Tibetan and Chaidamu horses). Compared with other Chinese breeds, CKY horses present reduced nucleotide diversity (θπ)...
Analyses of whole-genome sequences from 185 North American Thoroughbred horses, spanning 5 generations. Whole genome sequences (WGS) of 185 North American Thoroughbred horses were compared to quantify the number and frequency of variants, diversity of mitotypes, and autosomal runs of homozygosity (ROH). Of the samples, 82 horses were born between 1965 and 1986 (Group 1); the remaining 103, selected to maximize pedigree diversity, were born between 2000 and 2020 (Group 2). Over 14.3 million autosomal variants were identified with 4.5-5.0 million found per horse. Mitochondrial sequences associated the North American Thoroughbreds with 9 of 17 clades previously identified among diverse breeds. Indi...
The Weight of Genetic Drift: A Pedigree-Based Evaluation of the Breton Horse Population in Brazil. The genetic diversity of Breton horses in Brazil is a critical concern, mainly due to the small population size and low number of births per year. Given that the inbreeding was overlooked by breeders for multiple generations, we estimated the genetic diversity of this population utilizing pedigree-based measures of population diversity. A total of 1394 six-generation pedigrees representing the full population of registered Breton horses in Brazil defined a total population (TP, = 2679), with horses born between 2000 and 2022, reproductively active and alive, as reported by the breed assoc...
Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies. The Icelandic horse and Exmoor pony are ancient, native breeds, adapted to harsh environmental conditions and they have both undergone severe historic bottlenecks. However, in modern days, the selection pressures on these breeds differ substantially. The aim of this study was to assess genetic diversity in both breeds through expected (HE) and observed heterozygosity (HO) and effective population size (Ne). Furthermore, we aimed to identify runs of homozygosity (ROH) to estimate and compare genomic inbreeding and signatures of selection in the breeds. Results: HO was estimated at 0.34 and 0.33...
Genetic Diversity and Population Structure of Dülmen Wild, Liebenthal and Polish Konik Horses in Comparison with Przewalski, Sorraia, German Draught and Riding Horses. The objective of the present study was to analyze the genetic diversity, individual-based assessment of population structure, and admixture in the Dülmen wild horse population in comparison to warmblood, coldblood, and primitive horse populations. The Dülmen wild horse is kept as a unique horse population in the Merfelder Bruch near Dülmen in Westphalia, Germany, and since 1856 has been managed by the Dukes of Croÿ. The Dülmen wild horse population is exposed to the natural conditions of the Merfelder Bruch all year round without human interventions for feeding and veterinary care. In the...
Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed. The Franches-Montagnes (FM) is the last native horse breed of Switzerland, established at the end of the 19th century by cross-breeding local mares with Anglo-Norman stallions. We collected high-density SNP genotype data (Axiom™ 670 K Equine genotyping array) from 522 FM horses, including 44 old-type horses (OF), 514 European Warmblood horses (WB) from Sweden and Switzerland (including a stallion used for cross-breeding in 1990), 136 purebred Arabians (AR), 32 Shagya Arabians (SA), and 64 Thoroughbred (TB) horses, as introgressed WB stallions showed TB origin in their pedigrees. The aim of ...
Evaluation of breeding strategies to reduce the inbreeding rate in the Friesian horse population: Looking back and moving forward. In the past, small population sizes and unequal ancestor contributions have resulted in high inbreeding rates (ΔF) in the Friesian horse. Two decades ago, the studbook implemented a mating quota and started publishing individual kinships and reduced ΔF below 1% per generation. However, since then, the breeding population size has decreased and this raises the question whether current breeding strategies are sufficient to keep ΔF below desired rates. The aim of this study was to (1) reflect on past inbreeding trends and their main determinants, using pedigree analysis and (2) evaluate the ef...
Population genomics provide insight into ancestral relationships and diversity of the feral horses of Theodore Roosevelt National Park. Theodore Roosevelt National Park (TRNP) manages a herd of feral horses () which was present on the landscape prior to the establishment of the park. The population presents a unique scenario in that it has experienced fairly intensive and well-documented management since the park's establishment, including herd size reductions, intentional introduction of diversity, and subsequent attempts to remove introduced lineages. This provides an interesting case study on the genetic effects of diverse evolutionary forces on an isolated feral population. To explore the effects of these forces and clarif...
Population structure and genetic diversity of Polish Arabian horses based on pedigree data. With a history tracing back to at least the 18th century and a substantial global influence on various breeds, Polish Arabian horse population is of paramount importance for both breeders and conservationists. However, its genetic makeup and the population dynamics are still not well understood. This study presents an analysis of the modern Polish Arabian horse population using pedigree data, focusing on the breed's genetic diversity and population structure. Our analysis encompassed 1 498 individuals defined as the reference population (RP) and their 11 065 ancestors, which resulted in the ...
Genome-wide analysis of population structure, effective population size and inbreeding in Iranian and exotic horses. Population structure and genetic diversity are the key parameters to study the breeding history of animals. This research aimed to provide a characterization of the population structure and to compare the effective population size (Ne), LD decay, genetic diversity, and genomic inbreeding in Iranian native Caspian (n = 38), Turkmen (n = 24) and Kurdish (n = 29) breeds and some other exotic horses consisting of Arabian (n = 24), Fell pony (n = 21) and Akhal-Teke (n = 20). A variety of statistical population analysis techniques, such as principal component analysis (PCA), discriminant analysis of...
Reproductive traits in Pura Raza Española mares manifest inbreeding depression from low levels of homozygosity. Inbreeding depression is a genetic phenomenon associated with the loss of fitness and mean phenotypic performance due to mating between relatives. Historically, inbreeding coefficients have been estimated from pedigree information. However, the onset of genomic selection programs provides large datasets of individuals genotyped using SNP arrays, enabling more precise assessment of an individual's genomic-level inbreeding using genomic data. One of the traits most sensitive to issues stemming from increased inbreeding is reproduction. This is particularly important in equine, in which fertility...
Relatedness and genomic inbreeding in a sample of Timor ponies. Timor ponies (TP) were first shipped to Australia in the early 1800s and were highly valued as transport and pack animals, which resulted in TPs contributing to the development of Australian horse breeds. Today, while the exact number of TPs in Australia is currently unknown, there has been recent interest in establishing a domestic breeding program for Australian TPs. The aim of this study was to evaluate the relatedness of a sample of TPs, as well as provide estimates of genomic inbreeding levels to better inform the feasibility of using these animals as founders for a domestic breeding prog...
Does inbreeding contribute to pregnancy loss in Thoroughbred horses? Excessive inbreeding increases the probability of uncovering homozygous recessive genotypes and has been associated with an increased risk of retained placenta and lower semen quality. No genomic analysis has investigated the association between inbreeding levels and pregnancy loss. Objective: To compare genetic inbreeding coefficients (F) of naturally occurring Thoroughbred Early Pregnancy Loss (EPLs), Mid and Late term Pregnancy Loss (MLPL) and Controls. The F value was hypothesised to be higher in cases of pregnancy loss (EPLs and MLPLs) than Controls. Methods: Observational case-control st...
The Genetic Diversity of Horse Native Breeds in Russia. Horses were domesticated later than other farm animals. Horse breeds have been selectively developed by humans to satisfy different needs and purposes. The factory and indigenous breeds are of particular interest, having been bred in purity for many centuries without the addition of foreign blood. Data from 31 stud farms, as well as ranches, located in fifteen regions of the Russian Federation were used in this work. DNA was sampled from 102 stallions of 11 breeds: Arabian, Akhal-Teke, Don, Orlov Trotter, Vladimir Heavy Draft, Russian Heavy Draft, Soviet Heavy Draft, Kabardin, Yakut, Tuva, and...
Should performance at different race lengths be treated as genetically distinct traits in Coldblooded trotters? Speed, in the form of racing time per kilometre (km), is a performance trait of the Swedish-Norwegian Coldblooded trotter included in the joint Swedish-Norwegian genetic evaluation. A few popular stallions have dominated Coldblooded trotter breeding, which has led to an increasing average relationship between individuals in the population. This study investigated the scope for broadening the breeding goal by selecting for racing time per km over different race lengths (short: 1640 m, medium: 2140 m and long: 2640 m), as this could encourage the use of breeding sires that are less related...
Orthopedic Diseases in the Pura Raza Española Horse: The Prevalence and Genetic Parameters of Angular Hoof Deviations. Abnormalities in hoof shape are usually connected with limb conformation defects. The role of angular hoof deviations is important for longevity in sports competitions and is increasingly recognized as a factor associated with lameness in performance horses. In this paper, we measured the prevalence of four defects related to the angulation of the hoof in the Pura Raza Española horse (PRE): splay-footed forelimb (SFF), pigeon-toed forelimb (PTF), splay-footed rear limb (SFR), and pigeon-toed rear limb (PTR). A total of 51,134 animals were studied, of which only 15.75% did not have any of the ...
Historic Horse Family Displaying Malformations of the Cervicothoracic Junction and Their Connection to Modern German Warmblood Horses. Malformations of the equine cervicothoracic junction affect the C6 and C7 cervical vertebrae, the T1 thoracic vertebra and in variable extent the first and second sternal ribs. To date, the clinical impact of this malformation, its prevalence and mode of inheritance in equine populations are not yet determined. We examined five skeletons for signs of malformation of the cervicothoracic junction, including three skeletons from widely used Thoroughbred stallions affected with the malformation and two skeletons serving as a comparison. The three affected historical horses were the Thoroughbred st...
Phenotypic and Genetic Study of the Presence of Hair Whorls in Pura Raza Español Horses. Hair whorls are a hereditary feature in horses that may be associated with temperament and coat color. Hair whorls are described as changes in the hair pattern and may take various forms, such as circular and linear whorls. We first carried out a frequency analysis of hair whorls (circular and linear). Next, a Generalized Non-Linear Model was computed to assess the significance of some potential influencing factors, and a genetic parameter estimation was performed. ENDOG software v4.8 was used to estimate the inbreeding coefficient of all the animals analyzed. It was more common to find horses...
Unravelling of the genetic diversity, population structure, and phylogenetic relationships of the indigenous horse breeds of Pakistan. The current study aimed to evaluate the genetic diversity, level of admixture, and phylogenetic relationship, of the Pakistani horse breeds, along with their morphological characterization. Data for the body measurements showed that Morna horses had the highest values of body height, body length, chest girth, leg length, and head length, whereas the Baluchi horses had the lowest values for these traits. For the genetic diversity 64 animals, 15/breed except for Baluchi(14) and Topras(05), were genotyped by using the 17-plex equine genotyping kit. The AMOVA results showed that 13% of genetic div...
Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach. The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of th...
Genome-Wide Single-Nucleotide Polymorphism-Based Genomic Diversity and Runs of Homozygosity for Selection Signatures in Equine Breeds. The horse, one of the most domesticated animals, has been used for several purposes, like transportation, hunting, in sport, or for agriculture-related works. Kathiawari, Marwari, Manipuri, Zanskari, Bhutia, Spiti, and Thoroughbred are the main breeds of horses, particularly due to their agroclimatic adaptation and role in any kind of strong physical activity, and these characteristics are majorly governed by genetic factors. The genetic diversity and phylogenetic relationship of these Indian equine breeds using microsatellite markers have been reported, but further studies exploring the SNP d...
Construction of an individual identification panel for horses using insertion and deletion markers. Individual identification and paternity testing are important for avoiding inbreeding in the management of small populations of wild and domestic animals. In horse racing industries, they are extremely important for identifying and registering individuals and doping control to ensure fair competition. In this study, we constructed an individual identification panel for horses by using insertion and deletion (INDEL) markers. The panel included 39 INDEL markers selected from a whole-genome INDEL database. Genotyping of 89 Thoroughbreds showed polymorphisms with minor allele frequencies (MAFs) of...
The Genetic Diversity of Stallions of Different Breeds in Russia. The specifics of breeding and selection significantly affect genetic diversity and variability within a breed. We present the data obtained from the genetic analysis of 21 thoroughbred and warmblood horse breeds. The most detailed information is described from the following breeds: Arabian, Trakehner, French Trotter, Standardbred, and Soviet Heavy Horse. The analysis of 509,617 SNP variants in 87 stallions from 21 populations made it possible to estimate the genetic diversity at the genome-wide level and distinguish the studied horse breeds from each other. In this study, we searched for heter...
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...
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...
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...
Impact of inbreeding and genetic parameter estimates for seminal traits in Lusitano horses. The objectives of this study were to establish baseline information for seminal traits in Lusitano stallions, to assess the impact of inbreeding, interval between collections and age on semen quality during the breeding and non-breeding seasons, and to estimate the corresponding genetic parameters. A total of 2129 ejaculates by 146 Lusitano stallions used for artificial insemination, obtained from four equine reproduction centers distributed throughout Portugal, over a period of 14 years (2008-2021), were included in the study. The seminal traits analyzed, and the corresponding means and stand...
Evaluation of genetic diversity using 31 microsatellites in Miyako horses. The Miyako horse is a native Japanese horse breed. As with other native Japanese horses, the number of Miyako horses decreased due to mechanization and motorization, which reduced their roles, with just 14 in 1980. Although their population had increased to 55 horses by 2021, a further increase in their numbers is required to avoid extinction. Recently, their breeding has involved natural mating during group grazing; therefore, pedigree management has been difficult, and individual identification has been inconclusive. With the aim of formulating an effective breeding plan, this study used mic...
Inbreeding depression and durability in the North American Thoroughbred horse. The proportion of the genome containing runs of homozygosity (ROH) affects production traits in livestock populations. In European and Australasian Thoroughbreds inbreeding, quantified using ROH (F ), is associated with the probability of ever racing. Here, we measured F using 333 K SNP genotypes from 768 Thoroughbred horses born in North America to evaluate the effect of inbreeding on racing traits in that region. Among North American horses, F was not associated (p = 0.518) with the probability of ever racing but was significantly associated with the number of race starts (p = 0.002). ...
