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.
Brandon RB, Giffard JM, Bell K.Single nucleotide polymorphisms (SNPs) in exons 13, 15 and 16 of equine transferrin for common, rare and mutant variants were investigated. Compared with previous work a further 13 SNPs have been identified, allowing for the two previously identified clades to be subdivided into 11 groups. A combination of one or more of eight SNPs can be used to classify the equine variants into these 11 groups, since most are co-inherited. Putative sites of glycosylation in exons 13 and 16 showed no polymorphism, suggesting that presence or absence of sugar moieties does not lead to electrophoretic variation...
Archambault D, Laganière G, St-Laurent G.The genetic variation in equine arteritis virus (EAV) nonstructural (NS) protein-encoding open reading frames (ORF) 3 and 4 genes was investigated. Nucleotide and deduced amino acid sequences from seven different EAV isolates (one European, one American and five Canadian isolates) and the Arvac vaccine strain were compared with those of the Bucyrus reference strain. ORF 3 nucleotide and amino acid sequence identities amongst these isolates (including the Arvac vaccine strain) and the Bucyrus reference strain ranged from 85.6 to 98.8%, and 85.3 to 98.2%, respectively, whereas ORF 4 nucleotide a...
Woolf CM.Arabian bay horses manifest, on the average, more common white markings in their hind legs than their forelegs (anteroposterior asymmetry) and more common white markings in their left legs than their right legs (directional asymmetry). To determine if genetic variation exists for these types of asymmetry, the phenotypic response was studied in bay foals when their dams and sires were selected for the directions of fore-hind and left-right differences. In the fore-hind studies, the quantitative shifts in the bay foals were in the direction specified by the selection scheme and the observed devi...
Falge R, Ehling C, Niemann H.The conservation of endangered breeds as live animals is at present the main national strategy of the government and breeding organizations to maintain genetic diversity. Fourty-three breeds and some old strains of cattle, pig, sheep, goat and horses are currently involved. Cryopreservation and banks for sperm, embryos or DNA are another type of genetic material which could subsequently be used for breeding and production in agriculture. Present semen banks involve 9 endangered cattle breeds and also a small amount of deep-frozen sperm of some endangered sheep and horse breeds. Only 2 embryo b...
Balasuriya UB, Timoney PJ, McCollum WH, MacLachlan NJ.The variation and phylogenetic relationship of open reading frame 5 (ORF5) of 3 different laboratory strains of the original prototype Bucyrus strain of equine arteritis virus (EAV), the modified live virus vaccine (ARVAC, Fort Dodge Laboratories), and 18 field isolates of EAV from North America and Europe were determined by comparison of their gene sequences. The viruses differed from the published sequence by between 3 (99.6% homology) and 94 (87.8%) nucleotides and by between 3 (98.8%) and 24 (90.6%) amino acids. The field isolates differed from each other by between 2 (99.7%) and 110 (85.7...
Ishida N, Oyunsuren T, Mashima S, Mukoyama H, Saitou N.The noncoding region between tRNAPro and the large conserved sequence block is the most variable region in the mammalian mitochondrial DNA D-loop region. This variable region (ca. 270 bp) of four species of Equus, including Mongolian and Japanese native domestic horses as well as Przewalskii's (or Mongolian) wild horse, were sequenced. These data were compared with our recently published Thoroughbred horse mitochondrial DNA sequences. The evolutionary rate of this region among the four species of Equus was estimated to be 2-4 x 10(-8) per site per year. Phylogenetic trees of Equus species demo...
Bogumil R, Hunter CL, Maurus R, Tang HL, Lee H, Lloyd E, Brayer GD, Smith M, Mauk AG.The interaction of azide with variants of horse heart myoglobin (Mb) has been characterized by Fourier transform infrared (FTIR), electron paramagnetic resonance (EPR), and UV-VIS absorption spectroscopy and by molecular modeling calculations. Distal histidine variants (His64Thr, His64Ile, His64Lys) and charged surface variants (Val67Arg, Lys45Glu, Lys45Glu/Lys63Glu) were included in this study. All variants, with the exception of Val67Arg, have a lower azide affinity than the wild-type protein. Analysis of the temperature dependence of the FTIR spectra (277-313 K) revealed that the wild-type ...
Murphy TW, McCollum WH, Timoney PJ, Klingeborn BW, Hyllseth B, Golnik W, Erasmus B.Equine arteritis virus (EAV), a non-arthropod borne togavirus, has been shown to have a global distribution. To date, no major antigenic variation has been demonstrated between EAV isolates from different geographic origins. In this study, the genomic RNA of EAV isolates obtained from horses of different breeds in various countries around the world was oligonucleotide fingerprinted. Comparisons of these fingerprints were used to determine the extent of genomic variation among such isolates. Comparisons among isolates from North American horses revealed, for the most part, oligonucleotide homol...
Dubrovskaia RM, Starodumov IM, Bannikova LV.The estimation of genetic differentiation between 27 horses breeds originated in USSR, based on serum proteins polymorphism (loci Tf, Al, Es) is shown. Genetical variability among aborigine breeds is higher then among cultural ones. The erosion of gene pool of Przewalski's Horse is explained by special history of this population and a few horses in analyzing group. Genetic distances reflect the directions and intensity of breeding. High genetical distances between Przewalski's Horse, Shetland Pony and other horses obtained could be explained by overcoming the "bottle neck" of selections in bre...
Ellegren H, Johansson M, Sandberg K, Andersson L.We have isolated equine microsatellites by screening a genomic library with (TG)n and (TC)n probes. TG microsatellites were found to be more abundant than TC repeats, with an estimated frequency of one per 100,000bp. Sequence analysis of eight TG-positive clones revealed varying structures of the repeat regions; perfect stretches of TG repeats, imperfect stretches of TG repeats and compound regions of TG and TC repeats. Five loci were analysed by PCR and showed extensive polymorphism; three to seven alleles and heterozygosities of 0.40-0.76 were observed when screening 20-30 unrelated individu...
Kashi Y, Tikochinsky Y, Genislav E, Iraqi F, Nave A, Beckmann JS, Gruenbaum Y, Soller M.Southern blots of genomic DNA from a variety of species digested by restriction endonucleases having a four-bp specificity, were probed with a bovine genomic clone consisting of seven tandem poly-TG stretches separated by a 29bp linker sequence. Highly variable DNA 'fingerprint' patterns were obtained in chicken, sheep, and horse, moderately variable DNA 'fingerprints' in mouse and man, and a monomorphic pattern in Drosophila. In chicken, horse and man a (TG)10 synthetic oligonucleotide probe gave results identical to those given by the bovine probe. Furthermore, in chicken the DNA fingerprint...
Clegg JB.The sequences of the linked alpha 2- and alpha 1-globin genes of the equine BI and BII haplotypes are greater than 99% identical within a 1.2-kb region extending from approximately 75 bp upstream of the putative cap site to a point approximately 150 bp 3' to the poly A addition signal. Differences between the alpha 2 and alpha 1 genes that are common to both haplotypes indicate that a major gene conversion occurred approximately 12 Myr ago and that this has been followed by shorter, more localized, conversions. Interhaplotype (allelic) comparisons at the alpha loci suggest that the BI and BII ...
Malmheden Yman I, Sandberg K.Meat from the species horse, donkey and their hybrids, mule/hinny, can be reliably identified by determination of genetic variants of serum albumin by starch gel electrophoresis of meat extracts. Staining of the starch gel for carboxylesterase activity permits differentiation of most horses from donkeys while mules/hinnies cannot be distinguished from horses by their esterase activity alone.
Cothran EG, MacCluer JW, Weitkamp LR, Bailey E.American Standardbred horses are divided into two groups based upon gait: the trot and the pace. The tendency to trot (diagonally opposite legs moving forward together) or pace (the two legs on the same side of the body moving forward together) appears to be genetically determined, although no formal genetic analysis has been undertaken. There is nearly complete assortative mating for gait; however, about 20% of the offspring sired by trotters are registered as pacers, while fewer than 1% of those sired by pacers are registered as trotters. Electrophoretically detectable genic variation at 13 ...
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...
Atroshchenko M, Dementieva N, Shcherbakov Y, Nikolaeva O, Azovtseva A, Ryabova A, Nikitkina E, Makhmutova O, Datsyshin A, Zakharov V, Zaitsev A.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...
Saito I, Nakamura K, Tozaki T, Hano K, Takasu M.Concerns have been raised about the loss of genetic diversity in Japanese native horses because of their declining populations. In this study, we investigated the genetic variation of four genes, myostatin (MSTN), ligand-dependent nuclear receptor corepressor like (LCORL), doublesex and mab-3 related transcription factor 3 (DMRT3), and 5-hydroxytryptamine receptor 1A (HTR1A), which are associated with horse phenotypic traits, in six Japanese horse breeds (Hokkaido, Kiso, Noma, Misaki, Tokara, and Yonaguni). MSTN, LCORL, DMRT3, and HTR1A showed polymorphisms in the Kiso; Hokkaido and Noma; Hokk...
Gravey F, Sévin C, Castagnet S, Foucher N, Maillard K, Tapprest J, Léon A, Langlois B, Le Hello S, Petry S.Klebsiella pneumoniae is a major cause of infections and reproductive disorders among horses, ranked in recent French studies as the sixth most frequently isolated bacterial pathogen in equine clinical samples. The proportion of multidrug-resistant (MDR) K. pneumoniae is therefore significant in a context where MDR K. pneumoniae strains are considered a major global concern by the World Health Organization. Unassigned: In this study, we used a genomic approach to characterize a population of 119 equine K. pneumoniae strains collected by two laboratories specialized in animal health in Normandy...
Otgonsuren D, Amgalanbaatar T, Narantsatsral S, Enkhtaivan B, Munkhgerel D, Zoljargal M, Davkharbayar B, Myagmarsuren P, Battur B, Battsetseg B....Equine piroplasmosis is a tick-borne disease caused by Theileria equi and Babesia caballi in horses. Because of its impact on horse industry, control of this disease is crucial for endemic countries. The control of equine piroplasmosis may be influenced by the genotypic diversity of T. equi and B. caballi. Mongolia, a country with a thriving livestock industry, is endemic for T. equi and B. caballi. However, nationwide epidemiological surveys have not been conducted to determine the current status of infections and genetic diversity of these two parasite species. Therefore, the objective of th...
Bazvand B, Rashidi A, Zandi MB, Moradi MH, Rostamzadeh J.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...
Marín Navas C, Delgado Bermejo JV, McLean AK, León Jurado JM, Camacho Vallejo ME, Navas González FJ.The historical increase in the occurrence of extreme weather events in Spain during the last thirty years makes it a perfect location for the evaluation of climate change. Modeling the effects of climate change on domestic animals' genetic diversity may help to anticipate challenging situations. However, animal populations' short life cycle and patent lack of historical information during extended periods of time drastically compromise the evaluation of climate change effects. Locally adapted breeds' gene pool is the base for their improved resilience and plasticity in response to climate chan...
Klecel W, Kloch M, Wojciechowska M, Gajewska M, Martyniuk E.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 ...
Sigurðardóttir H, Ablondi M, Kristjansson T, Lindgren G, Eriksson S.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...
Duderstadt S, Distl O.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...
Medeiros BB, Barcelos KMC, Andrade MO, Cristina da Paz Carvalho M, Miranda VR, de Oliveira Maia K, Reinhardt S, Patterson Rosa L.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...
Liu YK, Fu WW, Wang ZY, Pei SW, Li KH, Wu WW, Le MZ, Yue XP.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)...
Parsad R, Bagiyal M, Ahlawat S, Arora R, Gera R, Chhabra P, Sharma U.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...
Ahlawat S, Sharma U, Niranjan SK, Chhabra P, Arora R, Sharma R, Singh KV, Vijh RK, Mehta SC.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...
Stejskalova K, Vychodilova L, Janova E, Oppelt J, Horin P.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...
Han J, Shao H, Sun M, Gao F, Hu Q, Yang G, Jafari H, Li N, Dang R.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...
Wang Y, Tang C, Xue P, Yang N, Sun X, Serik K, Assanbayer T, Shamekova M, Kozhanov Z, Sapakhova Z, Khurramovich JK, Zhou X, Kairat I, Muhatai G. 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 ...
Sievers J, Distl O.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 ...
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...
