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Topic:Genetic Diversity
Genetic diversity in horses refers to the variation in genetic characteristics within and among populations of horses. This diversity is shaped by factors such as breeding practices, geographic distribution, and historical population dynamics. Genetic diversity is measured using various molecular markers and provides insights into the evolutionary history, population structure, and adaptability of horse breeds. It influences traits such as disease resistance, fertility, and performance. This page compiles peer-reviewed research studies and scholarly articles that explore the assessment, implications, and conservation of genetic diversity in equine populations.
Genetic Diversity in Domestic Horses: Temporal Patterns, the Influence of Assisted Reproductive Technologies, and Implications for the American Quarter Horse. Genetic diversity is the heritable variation within and among populations and is essential for the long-term health and selection potential of domestic horses. Previous studies show diversity across breeds is shaped by effective population size, founder events, artificial selection, and levels of inbreeding. While some closed-studbook breeds retain moderate genetic diversity, others have experienced rapid losses due to popular-sire effects and recent and extensive inbreeding. Even so, mare lines continue to help maintain genetic diversity within these populations. Assisted Reproductive Technol...
Genetic diversity of horses of the Sargarinsko-Alexeevskaya and Irmen cultures of the Ob-Irtysh region of Western Siberia and their genetic proximity to modern horses of indigenous breeds. Genetic diversity of horses of the Sargarinsko-Alexeevskaya and Irmen cultures of the Ob-Irtysh region of Western Siberia and their genetic proximity to modern horses of indigenous breeds. Генетическое разнообразие лошадей саргаринско-алексеевской и ирменской культур Западной Сибири и их генетическое родство с современными лошадьми аборигенных пород.
Genetic variability and associations of Trakehner and other horse populations in Lithuania. To obtain genetic parameters relevant for the management of animal genetic resources, this study provides a comparative characterization of the Trakehner (TRAK) horse population in relation to four other horse populations maintained in Lithuania - Arabian (ARAB), Baltic Warmblood (BW), Lithuanian Warmblood (LW), and Zemaitukai (ZEM). These populations represent diverse histories, selection goals, and breeding practices. Pedigree data ( 22 666) and parentage verification genetic data based on blood group markers ( 1293) were used to evaluate genetic diversity, population structure, and inter-...
Genetic diversity of Dermacentor nitens (Acari: Ixodidae) collected on horses from western Cuba. The tropical horse tick, Dermacentor nitens Neumann, 1897, has a wide distribution throughout the Neotropics, and is a vector of protozoan haemoparasites that cause equine piroplasmosis. Despite this, little is known about the genetic diversity of this tick species, particularly in Cuba, where horses are important domestic animals used in agriculture and for transportation. The objective of this study was to assess the magnitude of genetic variation in 115 D. nitens adults (57 females and 58 males) collected from horses in the Cuban province of Mayabeque using sequence data of two mitochondria...
High frequency and high genetic diversity of Pneumocystis sp. in foals. Twenty-two foals, aged one to seven months, which died from interstitial pneumonia (15 foals) or unrelated illnesses and injuries (7 foals), were enrolled in this study. Sampling of the lungs was performed post-mortem for a total of 52 specimens. Pneumocystis was detected in 21/22 foals (48/52 specimens) using a PCR assay targeting the gene encoding the small subunit of the mitochondrial rRNA (mtSSUrRNA) of the horse-related Pneumocystis (Pneumocystis sp. 'Equus ferus caballus'). The sequencing of the PCR products was successful in 34/48 specimens. The sequences were identical to the horse-rel...
Genomic diversity and structure in arabian horses revealed by whole-genome sequencing: establishment of an allele frequency database of common genetic variation. BACKGROUND: The Arabian horse is a culturally and historically influential breed that has contributed to the development of many modern horse populations. However, genomic resources for this breed remain limited, particularly population-level allele frequency datasets that support studies of genetic diversity, selection, and disease. The aim of this study was to generate a comprehensive allele frequency database for Arabian horses using representative sampling and high-coverage whole-genome sequencing. RESULTS: We generated the first publicly available allele frequency database for the Arabian...
Pedigree Investigation of Polish Sport Horses in Show Jumping: Insights for Global Breeding. The aim of this study was to characterise the pedigree and genetic structure of Polish Sport Horses competing in Grand Prix show jumping events and to assess the implications for international sport horse breeding. Pedigrees of 513 horses were analysed, encompassing a total of 18,836 individuals over a maximum of 16 generations. The completeness and depth of the pedigrees allowed for a reliable estimation of inbreeding coefficients and genetic diversity. The mean inbreeding coefficient was low (0.645%), yet 82% of the horses exhibited some degree of inbreeding. The greatest loss of genetic var...
Population Structure and Genetic Diversity Among Lipizzan Mare Families in Hungary Based on Microsatellite Genotyping. 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...
Genetic Characterization of the Arabian Horse Population in Tunisia Using Microsatellites. The genetic diversity and population structure of Tunisian Arabian horses were assessed using highly polymorphic microsatellite markers, which are critical for conservation and breeding programs. Despite the cultural and economic importance of Arabian horses in Tunisia, molecular data supporting their management remain limited. In this study, DNA from 130 horses was genotyped with 17 ISAG-FAO-recommended microsatellites to evaluate diversity within Eastern and Western Arabian lineages and their relationship to Thoroughbreds. Eastern Arabians showed an average of 5.176 alleles per locus, observ...
Comparison between SNP array and imputed data to estimate population structure and ROH hotspots in horse breeds. Single nucleotide polymorphism (SNP) arrays are commonly used for studying the genomic structure and diversity of livestock breeds, but whole-genome sequencing (WGS) provides higher-resolution genomic data. Genotype imputation has become a standard practice for increasing the genomic resolution of association studies. This work aimed to extend imputation to biodiversity analyses, comparing SNP array data before and after imputation. A 40 k SNP dataset of 281 horses from 12 breeds (DS) was imputed to sequence-level using a reference panel of 327 sequenced individuals, generating approximately 9...
The genetic diversity and population structure of native horse breeds in Xinjiang, China. Xinjiang is a region renowned for its rich diversity of native horse breeds, making it one of the most affluent equine genetic resource areas in China. While prized for their high adaptability and tolerance to roughage, the conservation of these native breeds faces challenges from the introduction of external breeds and industrial changes. Furthermore, the unknown population structure of Xinjiang horse breeds has hindered effective conservation efforts. Unassigned: This study presents the first comprehensive Single Nucleotide Polymorphism (SNP) analysis of seven Xinjiang native horse breeds. W...
Exploring the Genetic Link Between Coat Colour and Morphological Traits: The Case of Peruano de Paso Horse. The Peruano de Paso is a horse breed renowned for its smooth gait, traditionally selected based on breeders' empirical knowledge. Recently, the frequency of chestnut horses, a recessive trait, has increased substantially within the official studbook. This study evaluated whether preference for chestnut coat colour has influenced morphological traits and genetic diversity within the breed. A total of 8376 records of seven morphological traits, collected by the Peruano de Paso Breeders Association over eight years, were analysed, along with a pedigree including 41,357 individuals. Morphological ...
Genetic Diversity of Equid Herpesvirus 5 in Temporal Samples from Mares and Their Foals at Three Polish National Studs. Equid herpesvirus 5 (EHV-5) comprises a group of heterogeneous viruses with a worldwide distribution. Primary infection typically occurs early in life, which is followed by latency and periodic recrudescence of the virus. The aim of this study was to determine the genetic variation of EHV-5 in individual animals over time and to determine the dynamics of EHV-5 spread among selected mare-foal pairs at three horse studs. The partial glycoprotein B () gene was amplified from archival nasal swab samples. Sequences from 3-5 clones from each PCR product were compared using identity matrix, phylogeny...
Population Structure and Genetic Diversity Among Shagya Arabian Horse Genealogical Lineages in Bulgaria Based on Microsatellite Genotyping. The Shagya Arabian horse breed was created to address the need of Imperial Hussars (Hungarian light horsemen) for a horse with the intelligence, essential characteristics, and endurance of the Arabian breed, but also of a bigger size and having a better weight-carrying capacity and jumping ability. The present study aimed to explore the genetic variability and population structure of the uninvestigated Shagya Arabian horse population in Bulgaria based on genotyping at 15 equine microsatellite markers. A total of 140 horses belonging to six genealogical lines (Dahoman, Gazal, Ibrahim, Kuhailan ...
Using STR Data to Investigate the Impact of the Studbook Cap on Genetic Diversity in the American Standardbred Horse from 1998 to 2021. 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...
Towards Practical Conservation Cloning: Understanding the Dichotomy Between the Histories of Commercial and Conservation Cloning. Over 40 years ago, scientists imagined ways cloning could aid conservation of threatened taxa. The cloning of Dolly the sheep from adult somatic cells in 1996 was the breakthrough that finally enabled the conservation potential of the technology. Until the 2020s, conservation cloning research efforts yielded no management applications, leading many to believe cloning is not yet an effective conservation tool. In strong contrast, domestic taxa are cloned routinely for scientific and commercial purposes. In this review, we sought to understand the reasons for these divergent trends. We scoured p...
Genomic insights into the genetic diversity and genetic basis of body height in endangered Chinese Ningqiang ponies. Genetic diversity in livestock and poultry is critical for adapting production systems to future challenges. However, inadequate management practices, particularly in developing countries, have led to the extinction or near extinction of several species. Understanding the genetic composition and historical background of local breeds is essential for their effective conservation and sustainable use. This study compared the genomes of 30 newly sequenced Ningqiang ponies with those of 56 other ponies and 104 horses to investigate genetic diversity, genetic differentiation, and the genetic basis o...
Genomic Patterns of Homozygosity and Genetic Diversity in the Rhenish German Draught Horse. The Rhenish German draught horse is an endangered German horse breed, originally used as working horse in agriculture. Therefore, the objective of this study was to evaluate the breed's genetic diversity using pedigree and genomic data in order to analyze classical and ancestral pedigree-based inbreeding, runs of homozygosity, ROH islands, and consensus ROH. Methods: We studied the genome-wide genotype data of 675 Rhenish German draught horses and collated pedigree-based inbreeding coefficients for these horses. The final dataset contained 64,737 autosomal SNPs. Results: The average number of ...
Identification of Genetic Relationships and Group Structure Analysis of Yanqi Horses. The Yanqi horse is a distinguished local breed in China, known for its robust physique and strong adaptability. However, due to insufficient breeding populations and a loosely structured breeding system, the number of Yanqi horses has been declining annually. To protect its genetic resources and develop scientific breeding strategies, this study aimed to analyze the genetic diversity, parentage relationships, and genetic structure of the Yanqi horse conservation population using microsatellite markers. A total of 117 Yanqi horses were selected for genotyping analysis using 16 microsatellite ...
Innate Immunity Toll-Like Triad TLR6-1-10 and Its Diversity in Distinct Horse Breeds. Toll-like receptors (TLRs) play important roles in innate immunity and developmental processes. Due to their nature as molecular pattern recognition receptors, their genetic diversity may reflect the effects of various pathogen pressures. Here, the extent of variability in the TLR1-6-10 gene cluster in three geographically and historically distinct breeds of horses was analysed. A genetically diverse group of representatives of 14 other horse breeds provided additional information on the variability of this gene cluster in the domestic horse. Altogether, 25 SNPs were identified in the TLR6-1-1...
Genetic Composition of Polish Hucul Mare Families: mtDNA Diversity. The Hucul horse breed formed in the region of the Eastern Carpathians, likely through the natural crossbreeding of oriental horses. After World War II, their population significantly decreased, leading to the breeding being based on only 14 female lines, whose founders often had unknown origins. To preserve the breed's unique characteristics, it is now part of a Genetic Resources Conservation Program, which prioritizes the maintenance of genetic diversity. This study aims to clarify the maternal relatedness of founder mares and assess genetic diversity using mitochondrial DNA (mtDNA). The hy...
Unraveling the maternal heritage: identifying the complex origins of indigenous Indian horse and pony breeds through mitochondrial genome analysis. This study explored the maternal genetic diversity of six indigenous Indian horse and pony breeds (Bhutia, Kathiawari, Manipuri, Marwari, Spiti, and Zanskari) using comprehensive mitochondrial genome (mitogenome) analysis. Blood samples from 53 horses across diverse agro-climatic zones of India were analyzed, revealing 36 distinct haplotypes, with a haplotype diversity of 0.889 and nucleotide diversity of 0.00347. These indices suggest significant maternal genetic diversity in Indian equines. A median-joining (MJ) network, based on the hypervariable region of the D-loop along with sequences of...
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)...
Unraveling the genetic and physiological potential of donkeys: insights from genomics, proteomics, and metabolomics approaches. Donkeys (Equus asinus) have played a vital role in agriculture, transportation, and companionship, particularly in developing regions where they are indispensable working animals. The domestication of donkeys marked a significant turning point in human history, as they became essential for transportation, agriculture, and trade, especially in arid and semi-arid areas where their resilience and endurance were highly valued. In modern society, donkeys are indispensable due to their diversified applications, including meat, dairy, medicine, and functional bioproducts, supporting economic, cultura...
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...
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...
