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.
Jlassi M, Dhifalli I, Ouled Ahmed H, Lasfar F, El Gtari M, Jemmali B.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...
Moghbeli Damane M, Ayatollahi Mehrgardi A, Esmailizadeh A, Momen M.Inbreeding is caused by mating between related individuals and is associated with reduced fitness and performance. Generally, in the horse population, inbreeding is caused by geographically restricted areas and intensive natural or artificial selection. For this reason, assessing accurate inbreeding is essential for developing and implementing effective breeding strategies aimed at preserving genetic diversity and reducing the harmful consequences of inbreeding. One of the most accurate approaches for assessing genomic inbreeding and autozygosity is through the analysis of runs of homozygosity...
Ripollés-Lobo M, Perdomo-González DI, Azor P, Valera M.Investigate the genetic inbreeding depression load (IDL) on two dressage traits and two conformational defects in horses. Unassigned: The dataset included performance records for Walk and Points per Reprise (PPR) (N:43,838) and conformation data for Closed and Convergent hocks (N:57,949). Pedigree information spanned over 400,000 individuals. Inbreeding coefficients (F, F6, Fk) and partial inbreeding coefficient (Fij) were computed to quantify the IDL using Bayesian approach. Linear and ordinal logistic regressions were used to assess the relationship between inbreeding and phenotypic values. ...
Luštrek B, Šimon M, Turk K, Bogičević S, Potočnik K.In small, closed populations such as the Lipizzan horse, maintaining genetic diversity while limiting inbreeding is a key challenge in conservation breeding. The Lipizzan is an indigenous Slovenian breed with a small population and restricted gene flow from other subpopulations. Inbreeding is traditionally monitored with pedigree-based coefficients, but these often underestimate realised autozygosity, particularly when pedigree depth is limited. This study compared pedigree-based inbreeding (F_PED) with four genomic estimators (F_HOM, F_ROH, F_HBD, F_GRM) in 329 Slovenian Lipizzan horses genot...
Karlau A, Azcona F, Molina A, Trigo P, Sánchez-Serrano JP, Demyda-Peyrás S.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 ...
Duderstadt S, Distl O.Dülmen wild horses are kept in a fenced wooden and marsh area around Dülmen in Westphalia, Germany, since 1856. Previous analyses supported early genetic divergence from other domesticated horse populations and the Przewalski horse. Therefore, the objective of this study was to evaluate genetic diversity using high-density genomic data. Methods: We collected 337 one-year-old male Dülmen wild horses, captured at 12 annual auctions, for genotyping on the Illumina GGP Equine Plus Beadchip. All analyses were performed for 63,123 autosomal SNPs. Results: On average, each horse had 27.96 ROH with...
Drögemüller M, Fouché N, Wyler M, Gurtner C, Meister SL, Neuditschko M, Jagannathan V, Gerber V, Leeb T.Hypertriglyceridemia (HTG) may be inherited and caused by variants in genes encoding enzymes of lipid metabolism. This study was prompted by the observation of eight Franches-Montagnes (FM) foals showing elevated plasma triglyceride levels and episodes of fatal acute pancreatitis. We termed this phenotype hypertriglyceridemia-induced pancreatitis (HIP). The affected foals were distantly related and inbred to a prominent stallion suggesting autosomal recessive inheritance. Whole genome sequencing of an affected foal identified a homozygous loss of function variant in LMF1 encoding lipase matura...
Ding W, Gong W, Bou T, Shi L, Lin Y, Shi X, Li Z, Wu H, Dugarjaviin M, Bai D.The core objective of racehorse breeding is to enhance the speed and endurance of the horses. The Grassland-Thoroughbred is an emerging horse breed developed in northern China in recent years, characterized by excellent speed performance, enduring stamina, and strong environmental adaptability. However, research on the genetic characteristics within this breed and the genes associated with athletic performance remains relatively limited. We conducted whole-genome resequencing of Grassland-Thoroughbred F1, F2, F3, and the crossbred population (CY) and obtained a total of 4056.23 Gb of high-qual...
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...
Asti V, Summer A, Ablondi M, Sartori C, Giontella A, Pilastro V, Mecocci S, Cappelli K, Mancin E, Oian A, Mantovani R, Capomaccio S, Sabbioni A.Horses have undergone extensive natural and artificial selection, shaping the diversity of breeds observed today. Native Italian breeds present unique traits influenced by natural selection, such as adaptation to harsh climates, or hoof strength, but face challenges due to population declines and the reduction of their original breeding purpose. This study focuses on five local Italian breeds: Bardigiano, Haflinger, Maremmano, Murgese, and Italian Heavy Draught Horse, to understand how selection has shaped their populations. A total of 1620 individuals were genotyped with a medium-density SNP ...
Barsi B, Oláh J, Posta J.The Hungarian Coldblood horse was developed in the 1920s by crossing local mares with draft horses imported from Belgium and France, and was approved as an official horse breed in 1954. The aim of the study was to analyze the quality of the pedigree, generation interval, gene origin, and inbreeding. The pedigree information was received from the Hungarian Coldblood Horse Breeding Association. The studbook data of the registered animals up to 2023 were evaluated. Two reference populations were chosen: horses having offspring in 1989 and 2023. The final database contained 21,699 horses. Pedigree...
Blohina NV, Khrabrova LA.Russia has a significant pedigree diversity of horse breeds with unique gene pools that are well adapted to a wide variety of harsh natural and climatic conditions, are characterized by universal performance and high productive qualities, and are of significant interest to the world horse breeding. Genetic studies of population diversity in horse breeding are very relevant, since many domestic horse breeds are under threat of extinction. Biomaterials (hair, blood, semen) from horses of 15 local breeds bred in the Russian Federation and neighboring countries (CIS) were selected for the research...
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...
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 ...
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 ...
Azcona F, Molina A, Demyda-Peyrás S.Analyzing genetic variability and inbreeding trends is essential for effective breed management in animal populations. To this, the characterization of runs of homozygosity (ROH) provides a good genomic approach to study the phenomena. The Polo Argentino (PA) breed, globally recognized as the best adapted to playing polo, is known for its strong influence of Thoroughbreds, intense selective breeding, and extensive use of reproductive biotechnologies. This study investigates the PA's genomic variability, by characterizing the ROH landscape and identifying ROH islands (ROHi) as potential genomic...
Błaszczak A, Stefaniuk-Szmukier M, Długosz B, Musiał AD, Olczak K, Ropka-Molik K. 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...
Watanabe M, Sato F, Innan H.We investigated the changes in inbreeding levels in Japanese Thoroughbred horses over the past 46 years. Our results show a significant increase in inbreeding over the past 30 years, primarily due to the influence of two sires, Northern Dancer and Sunday Silence. Northern Dancer's bloodline spread gradually through descendants like Northern Taste, leading to a slower increase in the inbreeding coefficient. In contrast, Sunday Silence was directly imported and became a leading sire, causing a rapid increase in his blood proportion and inbreeding coefficient. Our findings suggest that monitoring...
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)...
Bailey E, Finno CJ, Cullen JN, Kalbfleisch T, Petersen JL.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...
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...
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...
Gmel AI, Mikko S, Ricard A, Velie BD, Gerber V, Hamilton NA, Neuditschko M.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 ...
Steensma MJ, Doekes HP, Pook T, Derks MFL, Bakker N, Ducro BJ.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...
Thompson MA, McCann BE, Rhen T, Simmons R.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...
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 ...
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...
Laseca N, Ziadi C, Perdomo-Gonzalez DI, Valera M, Demyda-Peyras S, Molina A.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...
Peripolli E, Munari DP, Silva MVGB, Lima ALF, Irgang R, Baldi F.This review presents a broader approach to the implementation and study of runs of homozygosity (ROH) in animal populations, focusing on identifying and characterizing ROH and their practical implications. ROH are continuous homozygous segments that are common in individuals and populations. The ability of these homozygous segments to give insight into a population's genetic events makes them a useful tool that can provide information about the demographic evolution of a population over time. Furthermore, ROH provide useful information about the genetic relatedness among individuals, helping t...
Schubert M, Jónsson H, Chang D, Der Sarkissian C, Ermini L, Ginolhac A, Albrechtsen A, Dupanloup I, Foucal A, Petersen B, Fumagalli M, Raghavan M....The domestication of the horse ∼ 5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski's horse and found genetic structure within Eurasia in the Late Pleist...
McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM, Distl O, Guérin G, Hasegawa T, Hill EW, Leeb T, Lindgren G, Penedo MC, Røed KH....An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50-100 kb and reached background levels within 1-2 Mb. The extent of LD and the level of inbreeding were highest in the ...
Przewalski's horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still endangered, with just 2,109 individuals, one-quarter of which are in Chinese and Mongolian reintroduction reserves [1]. These horses descend from a founding population of 12 wild-caught PHs and possibly up to four domesticated individuals [2-4]. With a stocky build, an erect mane, and stripped and sho...
Science (New York, N.Y.)April 30, 2017
Volume 356, Issue 6336 442-445 doi: 10.1126/science.aam5298
Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK....The genomic changes underlying both early and late stages of horse domestication remain largely unknown. We examined the genomes of 14 early domestic horses from the Bronze and Iron Ages, dating to between ~4.1 and 2.3 thousand years before present. We find early domestication selection patterns supporting the neural crest hypothesis, which provides a unified developmental origin for common domestic traits. Within the past 2.3 thousand years, horses lost genetic diversity and archaic DNA tracts introgressed from a now-extinct lineage. They accumulated deleterious mutations later than expected ...
Metzger J, Karwath M, Tonda R, Beltran S, Águeda L, Gut M, Gut IG, Distl O.Modern horses represent heterogeneous populations specifically selected for appearance and performance. Genomic regions under high selective pressure show characteristic runs of homozygosity (ROH) which represent a low genetic diversity. This study aims at detecting the number and functional distribution of ROHs in different horse populations using next generation sequencing data. Methods: Next generation sequencing was performed for two Sorraia, one Dülmen Horse, one Arabian, one Saxon-Thuringian Heavy Warmblood, one Thoroughbred and four Hanoverian. After quality control reads were mapped t...
Leroy G, Mary-Huard T, Verrier E, Danvy S, Charvolin E, Danchin-Burge C.Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate. Results: Depending on breed and method, effective population sizes ranged from 15 to 133 ...
Cunningham EP, Dooley JJ, Splan RK, Bradley DG.The thoroughbred (TB) horse is one of the oldest breeds of domestic animals, with pedigree records spanning three centuries. Because the population is essentially closed, there is concern about loss of genetic variation. Here we report two parallel analyses. In the first, genetic variation in the current population is measured using data from 13 microsatellite loci in 211 horses with relationships calculated based on allele sharing. In the second analysis, pedigree information is used to calculate genetic relationships between animals based on shared ancestry. These two measures of relationshi...
Corbin LJ, Blott SC, Swinburne JE, Vaudin M, Bishop SC, Woolliams JA.Many genomic methodologies rely on the presence and extent of linkage disequilibrium (LD) between markers and genetic variants underlying traits of interest, but the extent of LD in the horse has yet to be comprehensively characterized. In this study, we evaluate the extent and decay of LD in a sample of 817 Thoroughbreds. Horses were genotyped for over 50,000 single nucleotide polymorphism (SNP) markers across the genome, with 34,848 autosomal SNPs used in the final analysis. Linkage disequilibrium, as measured by the squared correlation coefficient (r(2)), was found to be relatively high bet...
Todd ET, Ho SYW, Thomson PC, Ang RA, Velie BD, Hamilton NA.The Thoroughbred horse has played an important role in both sporting and economic aspects of society since the establishment of the breed in the 1700s. The extensive pedigree and phenotypic information available for the Thoroughbred horse population provides a unique opportunity to examine the effects of 300 years of selective breeding on genetic load. By analysing the relationship between inbreeding and racing performance of 135,572 individuals, we found that selective breeding has not efficiently alleviated the Australian Thoroughbred population of its genetic load. However, we found evidenc...
Tryon RC, White SD, Bannasch DL.Hereditary equine regional dermal asthenia (HERDA), a degenerative skin disease that affects the Quarter Horse breed, was localized to ECA1 by homozygosity mapping. Comparative genomics allowed the development of equine gene-specific markers which were used with a set of affected horses to detect a homozygous, identical-by-descent block spanning approximately 2.5 Mb, suggesting a recent origin for the HERDA mutation. We report a mutation in cyclophilin B (PPIB) as a novel, causal candidate gene for HERDA. A c.115G>A missense mutation in PPIB alters a glycine residue that has been conserved acr...
Grilz-Seger G, Neuditschko M, Ricard A, Velie B, Lindgren G, Mesarič M, Cotman M, Horna M, Dobretsberger M, Brem G, Druml T.Intensive artificial and natural selection have shaped substantial variation among European horse breeds. Whereas most equine selection signature studies employ divergent genetic population structures in order to derive specific inter-breed targets of selection, we screened a total of 1476 horses originating from 12 breeds for the loss of genetic diversity by runs of homozygosity (ROH) utilizing a 670,000 single nucleotide polymorphism (SNP) genotyping array. Overlapping homozygous regions (ROH islands) indicating signatures of selection were identified by breed and similarities/dissimilaritie...
McGivney BA, Han H, Corduff LR, Katz LM, Tozaki T, MacHugh DE, Hill EW.The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the w...
Mitton JB, Schuster WS, Cothran EG, De Fries JC.Specific formulations are derived for the correlation between the heterozygosity of a randomly mating parent and its offspring for a diallelic locus, and for the correlation when multiple loci are considered. The expected correlation is maximal, approaching r = 0.50, when allelic frequencies are highly asymmetric, and it is zero when the allelic frequencies are equal to 0.50. Parent-offspring correlations, up to a maximum of 0.50 for diallelic loci, indicate that levels of heterozygosity can respond to selection. Multilocus allozyme data from limber pine, Pinus flexilis, and from horses of sta...
Ablondi M, Dadousis C, Vasini M, Eriksson S, Mikko S, Sabbioni A.Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed ba...
Bizarria Dos Santos W, Pimenta Schettini G, Fonseca MG, Pereira GL, Loyola Chardulo LA, Rodrigues Machado Neto O, Baldassini WA, Nunes de Oliveira H....With the availability of high-density SNP panels and the establishment of approaches for characterizing homozygosity and heterozygosity sites, it is possible to access fine-scale information regarding genomes, providing more than just comparisons of different inbreeding coefficients. This is the first study that seeks to access such information for the Mangalarga Marchador (MM) horse breed on a genomic scale. To this end, we aimed to assess inbreeding levels using different coefficients, as well as to characterize homozygous and heterozygous runs in the population. Using Axiom ® Equine Genoty...
The Journal of heredityJanuary 3, 2018
Volume 109, Issue 4 384-392 doi: 10.1093/jhered/esx114
Druml T, Neuditschko M, Grilz-Seger G, Horna M, Ricard A, Mesaric M, Cotman M, Pausch H, Brem G.Within the scope of current genetic diversity analyses, population structure and homozygosity measures are independently analyzed and interpreted. To enhance analytical power, we combined the visualization of recently described high-resolution population networks with runs of homozygosity (ROH). In this study, we demonstrate that this approach enabled us to reveal important aspects of the breeding history of the Haflinger horse. We collected high-density genotype information of 531 horses originating from 7 populations which were involved in the formation of the Haflinger, namely 32 Italian Ha...
Grilz-Seger G, Druml T, Neuditschko M, Dobretsberger M, Horna M, Brem G.The sample ascertainment bias due to complex population structures remains a major challenge in genome-wide investigations of complex traits. In this study we derived the high-resolution population structure and levels of autozygosity of 377 Lipizzan horses originating from five different European stud farms utilizing the SNP genotype information of the high density 700 k Affymetrix Axiom™ Equine genotyping array. Scanning the genome for overlapping runs of homozygosity (ROH) shared by more than 50% of horses, we identified homozygous regions (ROH islands) in order to investigate the gene ...
Hall SJ.Accurate measures of effective population sizes (Ne ) in livestock require good quality data and specialized skills for their computation and analysis. Ne can be estimated by Wright's equation Ne =4MF/(M+ F) (M, F being sires and dams, respectively), but this requires assumptions which are often not met. Total census sizes Nc of livestock breeds are collated globally. This paper investigates whether estimates of Ne can be made from Nc ; this would facilitate conservation monitoring. Some Ne methodologies avoid the assumptions of Wright's equation and permit measurement, rather than estimation,...
Glowatzki-Mullis ML, Muntwyler J, Pfister W, Marti E, Rieder S, Poncet PA, Gaillard C.Genetic characterization helps to assure breed integrity and to assign individuals to defined populations. The objective of this study was to characterize genetic diversity in six horse breeds and to analyse the population structure of the Franches-Montagnes breed, especially with regard to the degree of introgression with Warmblood. A total of 402 alleles from 50 microsatellite loci were used. The average number of alleles per locus was significantly lower in Thoroughbreds and Arabians. Average heterozygosities between breeds ranged from 0.61 to 0.72. The overall average of the coefficient of...
Marín Navas C, Delgado Bermejo JV, McLean AK, León Jurado JM, Torres ARBYR, Navas González FJ.Genetic diversity and population structure were analyzed using the historical and current pedigree information of the Arabian (PRá), Spanish Purebred (PRE), and Hispano-Arabian (Há) horse breeds. Genetic diversity parameters were computed and a canonical discriminant analysis was used to determine the contributions of ancestor breeds to the genetic diversity of the Há horse. Pedigree records were available for 207,100 animals born between 1884 and 2019. Nei's distances and the equivalent subpopulations number indicated the existence of a highly structured, integrated population for the Há ...
Torfason EG, Thorsteinsdóttir L, Torsteinsdóttir S, Svansson V.The horse population in Iceland is a special breed, isolated from other horses for at least 1000 years. This provides an exceptional opportunity to investigate old and new pathogens in an inbred herd with few infectious diseases. We have developed a high sensitivity semi-nested PCR to study equid gammaherpesviruses 2 and 5 (EHV-2 and 5) in Iceland. The first PCR is group specific, the second type-specific, targeting a 113bp sequence in the glyB gene. DNA isolated from white blood cells and 18 different organs was tested for the presence of EHV-2 and 5. This was done in adult horses and foals, ...
The Journal of heredityNovember 2, 2005
Volume 96, Issue 6 670-678 doi: 10.1093/jhered/esi123
Solis A, Jugo BM, Mériaux JC, Iriondo M, Mazón LI, Aguirre AI, Vicario A, Estomba A.In the present study, genetic analyses of diversity and differentiation were performed on four Basque-Navarrese semiferal native horse breeds. In total, 417 animals were genotyped for 12 microsatellite markers. Mean heterozygosity was higher than in other horse breeds, surely as a consequence of management. Although the population size of some of these breeds has declined appreciably in the past century, no genetic bottleneck was detected in any of the breeds, possibly because it was not narrow enough to be detectable. In the phylogenetic tree, the Jaca Navarra breed was very similar to the Po...
Giontella A, Pieramati C, Silvestrelli M, Sarti FM.The Maremmano is an autochthonous Italian horse breed, which probably descended from the native horses of the Etruscans (VI century B.C.); the Studbook was acknowledged in 1980, and it includes 12 368 horses born from that year up to 2015. The aim of this study was to evaluate the effect of the selection program on the genetic variability of the Maremmano population; the analysis was performed using both the 'Endog v 4.8' program available at http://webs.ucm.es/info/prodanim/html/JP_Web.htm and in-house software on official pedigree data. Four Reference Populations were considered, and the mos...
Takasu M, Hiramatsu N, Tozaki T, Kakoi H, Nakagawa T, Hasegawa T, Huricha , Maeda M, Murase T, Mukoyama H.In order to contribute to conservation of the endangered Kiso horse, we clarified their genetic information using 31 microsatellite DNAs, and genotyped 125 horses, 83% of the existing breed. First, we clarified the current status of the horses. The horses were confirmed to have experienced rapid loss of population causing a bottleneck, and their effective population size was much smaller than their census size. Moreover, the number of alleles (6.3), observed heterozygosity (0.674), and expected heterozygosity (0.662) were in the same range as other endangered horses all over the world. Therefo...
Colpitts J, McLoughlin PD, Poissant J.Understanding inbreeding and its impact on fitness and evolutionary potential is fundamental to species conservation and agriculture. Long stretches of homozygous genotypes, known as runs of homozygosity (ROH), result from inbreeding and their number and length can provide useful population-level information on inbreeding characteristics and locations of signatures of selection. However, the utility of ROH for conservation is limited for natural populations where baseline data and genomic tools are lacking. Comparing ROH metrics in recently feral vs. domestic populations of well understood spe...
Larison B, Pinho GM, Haghani A, Zoller JA, Li CZ, Finno CJ, Farrell C, Kaelin CB, Barsh GS, Wooding B, Robeck TR, Maddox D, Pellegrini M, Horvath S.Effective conservation and management of threatened wildlife populations require an accurate assessment of age structure to estimate demographic trends and population viability. Epigenetic aging models are promising developments because they estimate individual age with high accuracy, accurately predict age in related species, and do not require invasive sampling or intensive long-term studies. Using blood and biopsy samples from known age plains zebras (Equus quagga), we model epigenetic aging using two approaches: the epigenetic clock (EC) and the epigenetic pacemaker (EPM). The plains zebra...
Schurink A, Shrestha M, Eriksson S, Bosse M, Bovenhuis H, Back W, Johansson AM, Ducro BJ.The spectrum of modern horse populations encompasses populations with a long history of development in isolation and relatively recently formed types. To increase our understanding of the evolutionary history and provide information on how to optimally conserve or improve these populations with varying development and background for the future, we analyzed genotype data of 184 horses from 9 Dutch or common horse populations in the Netherlands: The Belgian draft horse, Friesian horse, Shetland pony, Icelandic horse, Gelder horse, Groninger horse, harness horse, KWPN sport horse and the Lipizzan...
Polak G, Gurgul A, Jasielczuk I, Szmatoła T, Krupiński J, Bugno-Poniewierska M.Traditionally, pedigree-based relationship coefficients were used to manage inbreeding and control inbreeding depression that occurs within populations. The extensive incorporation of genomic data in livestock breeding creates the opportunity to develop and implement methods to manage populations at the genomic level. Consequently, the realized proportion of the genome that two individuals share can be more accurately estimated instead of using pedigree information to estimate the expected proportion of shared alleles. To make use of this improvement, in this study we evaluated the genomic inb...
Ablondi M, Vasini M, Beretti V, Superchi P, Sabbioni A.Genetic diversity is a key factor for both adaptation and response to selection. The loss of genetic diversity causes a decrease in individual fitness, and it has a dramatically negative effect on population lifespan in the long term. This study aimed at exploring the genetic diversity at pedigree level of the Bardigiano horse breed, which is a native breed from Italy shaped for living in rural areas. In 1977, the Bardigiano studbook was founded to preserve the breed and for improving its use for riding and draft purposes. Pedigree data contained 9,469 horses, of which 3,416 were alive. Demog...
