Pedigree analysis in horses involves the study of lineage and ancestry to understand genetic relationships and inheritance patterns. It is a tool used to track traits, performance potential, and hereditary diseases within horse populations. Pedigree records often include detailed information on the ancestors of a horse, going back several generations, and can help in making informed breeding decisions. This page assembles peer-reviewed research studies and scholarly articles that explore the methodologies, applications, and implications of pedigree analysis in equine breeding and genetics.
Li Y, Fu C, Yun X, Zhang H, Yang T, Feng M, Wang X, Qian S, Xing W, Yang R, Wu J, Liu Y, Zhao C.With growing demand for pedigree verification and breed management in horses (Equus caballus), reliable paternal lineage tools are essential. Y-chromosomal STRs (Y-STRs) have advantages over autosomal STRs due to paternal inheritance and lack of recombination. However, few validated loci and no standardised efficient genotyping systems limit their use. Current methods often require multiple reactions, increasing cost and labour. Thus, identifying informative Y-STR loci and developing a multiplex PCR system for cost-effective paternal lineage analysis is urgently needed. Objective: To identify ...
An SJ, Sohn Y, Forbes E, Ryu SH.Osteochondritis dissecans (OCD) is a common developmental orthopedic condition in Thoroughbred racehorses and although arthroscopic surgery is widely used for treatment, its long-term effects on race performance remain unclear. This retrospective study evaluated the effect of OCD surgery on race performance, compared the predictive power of pedigree and management variables and applied interpretable machine learning methods for forecasting race performance outcomes. Data were collected from 75 Thoroughbreds that underwent OCD surgery between 2015 and 2017 and 257 maternal siblings without reco...
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...
Pepper B, North E, Culwell J, Nicodemus MC, Cavinder C, Harvey K, Williams T.Due to the incorporation of the Golden American Saddlebred Horse Association (GASHA) into the American Saddlebred Horse and Breeders Association (ASHBA), breeding for coat color has become more challenging for horse breeders. However, with this merger, pedigree tracing can be of value in pinpointing foundation bloodlines within the GASHA that influence production of the golden coat phenotype. Objective: The study objective was to document the historical origins of the GASHA through pedigree tracing to determine the influence of dilution alleles that produce the golden coat phenotype. Methods: ...
Ricard A, Deretz S, Menard C, Priest BDS.The objective was to evaluate the genetic relationship between the surface temperature of regions of interest, measured using infrared images of young horses and functional longevity in jumping. This relationship was assessed by comparing the temperatures measured in the offspring of two groups of sires, one favourable and one unfavourable, to longevity. The study used a specific data collection protocol on a sample of 921 young progeny, before they began competing, of 141 extreme stallions, comprising 61 favourable and 80 unfavourable sires. These stallions had been selected based on estimate...
Taned M, Zandi MB, Salek Ardestani S, Abdoli M, Spangler ML.Race performance in Thoroughbred horses is influenced by both genetic and environmental factors. Understanding their genetic architecture is essential for designing effective breeding programs. Objective: This study aimed to estimate genetic parameters and trends for key performance traits in Iranian Thoroughbred racehorses. Methods: Performance data, including race completion time (RCT), rank at the end of the competition (REC), and average speed (AS), were obtained from the Iranian Equestrian Federation (2002-2021). Pedigree data from 14,391 individuals were analyzed using CFC software. Gene...
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 ...
Kim D, Lee S, Oyungerel B, Cho G.This study aimed to generate information for parentage testing in horse breeds using microsatellites (STRs) and single-nucleotide polymorphisms (SNPs). Genotype data were obtained from 189 horse hair root samples, including 38 Thoroughbreds (TBs), 17 Jeju horses (JHs), 20 Quarter horses (QHs), 21 American Miniatures (AMs), and 93 Mongolian horses (MHs), using 15 STR markers and 71 SNP markers. Comparative analysis revealed that the mean expected heterozygosity ranged from 0.468 (AM) to 0.491 (JH) for SNPs and from 0.695 (TB) to 0.791 (MH) for STRs. The mean observed heterozygosity ranged from ...
Gelinder Viklund Å, Blom Y, Eriksson S.The breeding goal of the Swedish Warmblood horse (SWB) is to produce internationally competitive horses in dressage and show jumping. In the current genetic evaluation, breeding values are estimated in multiple-trait animal models where competition performance is the target trait and results from two different young horse tests serve as indicator traits. However, preselection of horses, both for young horse tests and for competitions, is not considered in the current evaluation. The overall aim of this study was to analyse the all-or-none trait start status, in competition and in young horse t...
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...
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...
Ziadi C, Valera M, Laseca N, Perdomo-González D, Demyda-Peyrás S, de Los Terreros AR, Molina A. By simultaneously integrating both genotyped and non-genotyped animals into genetic evaluation, the single-step genomic BLUP method enhanced the accuracy of genetic assessments. This study aimed to compare the increase in prediction reliability (R) between restricted maximum likelihood (REML) and single-step genomic REML (ssGREML) in the Pura Raza Española (PRE) horse breed. The dataset comprised reproductive records for seven fertility traits from 47,502 females, with a total of 57,316 animals represented in the pedigree. A total of 4009 animals were genotyped using the EQUIGENE 90K SNP ar...
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...
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 ...
Santana ML, Franco TGB, Bignardi AB.Barrel racing is a competitive timed rodeo event that challenges horses and riders to complete a cloverleaf pattern around three barrels in the fastest time possible. In this study, we aimed to estimate the genetic parameters of barrel racing time (BRT) and evaluate the most suitable statistical model for its analysis. We compared a repeatability model and three random regression models (RRM) to analyse the longitudinal BRT data in Brazilian Quarter Horses. A total of 356,877 BRT records from 14,108 horses that competed in various events held across Brazil between 2010 and 2024 were analysed. ...
Novak BJ, Ryder OA, Houck ML, Walker K, Russell L, Russell B, Walker S, Arenivas SS, Aston L, Veneklasen G, Ivy JA, Koepfli KP, Rusnak A, Simek J....Cloning from historically cryopreserved cells offers a potential means to restore lost genetic variation or increase the representation of particular lineages within bottlenecked species, provided such biobanked materials are archived for such genetic rescue applications. One species for which cloning can provide genetic management benefits is Przewalski's horse, . All ~1800 living Przewalski's horses, distributed across ex situ breeding facilities and in situ reintroduction sites, are descended from one or more of the five founder lineages established by the 12 horses captured from the wild b...
Chapard L, Gorssen W, Meyermans R, Hooyberghs K, Buys N, Janssens S.Show jumping is a popular equestrian sport that requires a unique combination of jumping capacity and rideability. It has been shown that genetics play an important role in show jumping performance that has significant implications for horse breeding programmes. This gives an important opportunity for studbooks to breed horses with the potential to perform at the highest level in show jumping competitions. However, show jumping competitions are performed at various levels (from recreational to international level) but only national competition results are used by Warmblood studbooks in most ge...
Baville E, Carstanjen B, Thomas-Cancian A, Calgaro A, Bonnet N, Tiret L, Gache V, Abitbol M.Supernumerary digits, or polydactyly, have been described in various species including humans, wild and domestic animals. In horses, it represents the most common congenital limb malformation, which has only been described in isolated cases or nuclear families. Molecular aetiology has not been reported. Objective: To characterise the phenotype of a non-syndromic pre-axial polydactyly in a horse family and to decipher the inheritance pattern. Methods: Retrospective study. Methods: Forty-three members of the family including a previously reported polydactyl case were recruited. Available clinica...
Ziadi C, Demyda-Peyrás S, Valera M, Perdomo-González D, Laseca N, Rodríguez-Sainz de Los Terreros A, Encina A, Azor P, Molina A.The single-step best linear unbiased predictor (ssGBLUP) has emerged as a reference method for genomic selection in recent years due to its advantages over traditional approaches. Although its application in horses remains limited, ssGBLUP has demonstrated the potential to improve the reliability of estimated breeding values in livestock species. This study aimed to assess the impact of incorporating genomic data using single-step restricted maximum likelihood (ssGREML) on reliability (R) in the Pura Raza Española (PRE) horse breed, compared to traditional pedigree-based REML. Methods: The an...
Crisà A, Cardinali I, Giontella A, Silvestrelli M, Lancioni H, Buttazzoni L.Lipizzan is a famous horse breed dating back to 1580 when the original stud of Lipica was established by the Hasburg Archduke Charles II. Currently, the Italian State Stud of Lipizzan Horses (ASCAL) is a conservation nucleus managed through strict mating rules where mitochondrial DNA sequences are used to verify the correct assignment of mares to a historical pedigree maternal lineage. Here, we analyzed the D-loop sequences of Lipizzan horses from the ASCAL in Monterotondo (Rome, Italy) in order to confirm their pedigree assignment to known female founder families. The concurrent investigation...
Bussiman F, Richter J, Hidalgo J, Silva FFE, Ventura RV, Carvalho RSB, Mattos EC, Ferraz JBS, Eler JP, de Carvalho Balieiro JC.Gait visual scores are widely applied to horse breeding because they are a fast and easy phenotyping strategy, allowing the numeric interpretation of a complex biological process such as gait quality. However, they may suffer from subjectivity or high environmental influence. We aimed to investigate potential causal relationships among six visual gait scores in Campolina horses. The data included 5475 horses with records for at least one of the following traits: Dissociation (Di), Comfort (C), Style (S), Regularity (R), Development (De), and Gait total Scores (GtS). The pedigree comprised thre...
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...
Radovic L, Remer V, Rigler D, Felkel S, Brem G, Wallner B.The paternally inherited, male-specific part of the Y chromosome (MSY) is an ideal marker for studying the origin, genealogies, and historical connections of horse patrilines. Here, we performed fine-scaled MSY haplotype (HT) analysis in two Baroque horse breeds, the Lipizzaner and the Kladruber, both known for their long-standing tradition of sire line breeding and interconnected genealogies. We genotyped 95 MSY markers using KASP technology in 90 stallions representing all patrilines of both breeds. We identified 14 HTs across eight Lipizzaner sire lines and six HTs in eight Kladruber lines....
Padilha DAO, Padilha SF, Martins R, Scheffer BEM, Miliorini MR, Dias LT, Teixeira RA.This study aimed to estimate genetic parameters for race time in seconds and final ranking, as well as to analyze the genetic trends associated with race time. The study utilized a dataset consisting of 23,290 records of race times and final ranks at distances of 1,000, 1,600, and 2,000 m from 6,213 Thoroughbred horses from the São Paulo Jockey Club. Our model considered the year of the run, animal sex, race class, track conditions, the linear effect of horse weight and age, and the quadratic effect of age as fixed covariates. Random effects included direct additive genetic, animal permanent ...
Pepper B, North E, Foster M, Culwell J, Nicodemus MC, Cavinder C, Harvey K, Williams T.Registration numbers for the Palomino Horse Breeders of America (PHBA) have risen with the assistance of new registration guidelines. These changes in guidelines allowed for registration of any horse with a palomino body color, including those with unknown pedigrees. While this promoted registry growth, documenting the breed's orgins from those known pedigrees making up the breed's foundation is important with the introduction of unknown pedigrees. This can be accomplished using pedigree tracing, which is of particular value for color registries as the study of coat color patterns is plagued w...
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...
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...
Cieslak M, Pruvost M, Benecke N, Hofreiter M, Morales A, Reissmann M, Ludwig A.Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population r...
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...
Jamieson A, Taylor SC.Three general formulae calibrate the average capability of marker systems to dispute falsely reported pedigree records in uniparous species. The most familiar exclusion formula applies to paternity, although the same formula applies equally to maternity. Another formula faults the relationship of a single offspring with its putative parent; for example, where the genotype of the other parent is not available. The remaining formulae excludes both of the falsely recorded parents of a substituted offspring. Simplified forms of the three general formulae facilitate the calculation of maximal avera...
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...
Wallner B, Vogl C, Shukla P, Burgstaller JP, Druml T, Brem G.The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most wi...
Wallner B, Palmieri N, Vogl C, Rigler D, Bozlak E, Druml T, Jagannathan V, Leeb T, Fries R, Tetens J, Thaller G, Metzger J, Distl O, Lindgren G....The Y chromosome directly reflects male genealogies, but the extremely low Y chromosome sequence diversity in horses has prevented the reconstruction of stallion genealogies [1, 2]. Here, we resolve the first Y chromosome genealogy of modern horses by screening 1.46 Mb of the male-specific region of the Y chromosome (MSY) in 52 horses from 21 breeds. Based on highly accurate pedigree data, we estimated the de novo mutation rate of the horse MSY and showed that various modern horse Y chromosome lineages split much later than the domestication of the species. Apart from few private northern Euro...
Bower MA, McGivney BA, Campana MG, Gu J, Andersson LS, Barrett E, Davis CR, Mikko S, Stock F, Voronkova V, Bradley DG, Fahey AG, Lindgren G....Selective breeding for speed in the racehorse has resulted in an unusually high frequency of the C-variant (g.66493737C/T) at the myostatin gene (MSTN) in cohorts of the Thoroughbred horse population that are best suited to sprint racing. Here we show using a combination of molecular- and pedigree-based approaches in 593 horses from 22 Eurasian and North-American horse populations, museum specimens from 12 historically important Thoroughbred stallions (b.1764-1930), 330 elite-performing modern Thoroughbreds and 42 samples from three other equid species that the T-allele was ancestral and there...
Raudsepp T, Finno CJ, Bellone RR, Petersen JL.The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite-free centromeres provide unique models for mammalian centromer...
Nikiforov TT, Rendle RB, Goelet P, Rogers YH, Kotewicz ML, Anderson S, Trainor GL, Knapp MR.A new method for typing single nucleotide polymorphisms in DNA is described. In this method, specific fragments of genomic DNA containing the polymorphic site(s) are first amplified by the polymerase chain reaction (PCR) using one regular and one phosphorothioate-modified primer. The double-stranded PCR product is rendered single-stranded by treatment with the enzyme T7 gene 6 exonuclease, and captured onto individual wells of a 96 well polystyrene plate by hybridization to an immobilized oligonucleotide primer. This primer is designed to hybridize to the single-stranded target DNA immediately...
Hill EW, Bradley DG, Al-Barody M, Ertugrul O, Splan RK, Zakharov I, Cunningham EP.Mitochondrial DNA (mtDNA) D-loop sequences (381 bp) from 100 thoroughbreds in 19 of the most common matrilineal female families were used to reconstruct a founder female population for the thoroughbred ( approximately 1650-1750 AD). Seventeen haplotypes were found to have contributed to the 19 female lineages. In order to place the reconstructed founder population in wider historical context, we examined, using both single strand conformation polymorphism and direct sequence analysis, variation in a 343 bp mtDNA fragment in that population and 13 other horse populations of disparate provenance...
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...
The Journal of heredityOctober 15, 2003
Volume 94, Issue 5 374-380 doi: 10.1093/jhered/esg079
Tozaki T, Takezaki N, Hasegawa T, Ishida N, Kurosawa M, Tomita M, Saitou N, Mukoyama H.The genetic relationships of seven Japanese and four mainland-Asian horse populations, as well as two European horse populations, were estimated using data for 20 microsatellite loci. Mongolian horses showed the highest average heterozygosities (0.75-0.77) in all populations. Phylogenetic analysis showed the existence of three distinct clusters supported by high bootstrap values: the European cluster (Anglo-Arab and thoroughbreds), the Hokkaido-Kiso cluster, and the Mongolian cluster. The relationships of these clusters were consistent with their geographical distributions. Basing our assumpti...
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...
Felkel S, Vogl C, Rigler D, Dobretsberger V, Chowdhary BP, Distl O, Fries R, Jagannathan V, Janečka JE, Leeb T, Lindgren G, McCue M, Metzger J....Analysis of the Y chromosome is the best-established way to reconstruct paternal family history in humans. Here, we applied fine-scaled Y-chromosomal haplotyping in horses with biallelic markers and demonstrate the potential of our approach to address the ancestry of sire lines. We de novo assembled a draft reference of the male-specific region of the Y chromosome from Illumina short reads and then screened 5.8 million basepairs for variants in 130 specimens from intensively selected and rural breeds and nine Przewalski's horses. Among domestic horses we confirmed the predominance of a young'c...
Bowling AT, Del Valle A, Bowling M.Through DNA sequence comparisons of a mitochondrial D-loop hypervariable region, we investigated matrilineal diversity for Arabian horses in the United States. Sixty-two horses were tested. From published pedigrees they traced in the maternal line to 34 mares acquired primarily in the mid to late 19th century from nomadic Bedouin tribes. Compared with the reference sequence (GenBank X79547), these samples showed 27 haplotypes with altogether 31 base substitution sites within 397 bp of sequence. Based on examination of pedigrees from a random sampling of 200 horses in current studbooks of the A...
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...
Tozaki T, Kakoi H, Mashima S, Hirota K, Hasegawa T, Ishida N, Miura N, Choi-Miura NH, Tomita M.Microsatellite 15 TKY System was characterized for parentage verification of horse registry. The Microsatellite 15 TKY System was constructed by using 15 microsatellites, TKY279, TKY287, TKY294, TKY297, TKY301, TKY312, TKY321, TKY325, TKY333, TKY337, TKY341, TKY343, TKY344, TKY374, and TKY394, to provide stringent PCR-based microsatellite typing specifically optimized for multicolor fluorescence detection. The Microsatellite 15 TKY System showed good resolutions for 250 unrelated Thoroughbred horses, and the probability of exclusion (PE) at each microsatellite ranged from 0.437 to 0.621, resul...
Bower MA, Campana MG, Whitten M, Edwards CJ, Jones H, Barrett E, Cassidy R, Nisbet RE, Hill EW, Howe CJ, Binns M.The paternal origins of Thoroughbred racehorses trace back to a handful of Middle Eastern stallions, imported to the British Isles during the seventeenth century. Yet, few details of the foundation mares were recorded, in many cases not even their names (several different maternal lineages trace back to 'A Royal Mare'). This has fuelled intense speculation over their origins. We examined mitochondrial DNA from 1929 horses to determine the origin of Thoroughbred foundation mares. There is no evidence to support exclusive Arab maternal origins as some historical records have suggested, or a sign...
Kim KI, Yang YH, Lee SS, Park C, Ma R, Bouzat JL, Lewin HA.Historical records suggest that horses inhabiting the island of Cheju in Korea are descendants of Mongolian horses introduced in 1276. Other studies, however, suggest that horses may have been present on the island prior to the Mongolian introduction. To determine the origin of the Cheju horses we used a phylogenetic analysis of sequences of the mitochondrial DNA (mtDNA) D-loop region, including tRNA Pro and parts of tRNA thr and tRNA Phe sequences (1102-bp excluding the tandem repeat region). Maximum parsimony and neighbor-joining trees were constructed using sequences determined for seven Ch...
Gaffney B, Cunningham EP.Thoroughbred horses have been bred exclusively for racing in England since Tudor times and thoroughbred horse racing is now practised in over 40 countries and involves more than half-a-million horses worldwide. The genetic origins of the thoroughbred go back largely to horses imported from the Middle East and North Africa to England in the late seventeenth and early eighteenth centuries. Since the establishment of the Stud Book in 1791, the population has been effectively closed to outside sources, and over 80% of the thoroughbred population's gene pool derives from 31 known ancestors from thi...
Bowling AT, Eggleston-Stott ML, Byrns G, Clark RS, Dileanis S, Wictum E.A parallel testing of 4803 routine Quarter Horse parentage cases, using 15 loci of blood group and protein polymorphisms (blood typing) and 11 loci of dinucleotide repeat microsatellites (DNA typing), validated DNA markers for horse pedigree verification. For the 26 loci, taken together, the theoretical effectiveness of detecting incorrect parentage was 99.999%, making it extremely unlikely that false parentage would fail to be recognized. The tests identified incorrect parentage assignment for 95 offspring (2% of cases). Despite fewer loci, DNA typing was as effective as blood typing and, in ...
Finno CJ, Famula T, Aleman M, Higgins RJ, Madigan JE, Bannasch DL.Equine neuroaxonal dystrophy/equine degenerative myeloencephalopathy (NAD/EDM) is a neurodegenerative disorder affecting young horses of various breeds that resembles ataxia with vitamin E deficiency in humans, an inherited disorder caused by mutations in the alpha-tocopherol transfer protein gene (TTPA). To evaluate variants found upon sequencing TTPA in the horse, the mode of inheritance for NAD/EDM had to be established. Objective: NAD/EDM in the American Quarter Horse (QH) is caused by a mutation in TTPA. Methods: 88 clinically phenotyped (35 affected [ataxia score ≥2], 53 unaffected) QH...
Khanshour AM, Cothran EG.Maternal inheritance is an essential point in Arabian horse population genetics and strains classification. The mitochondrial DNA (mtDNA) sequencing is a highly informative tool to investigate maternal lineages. We sequenced the whole mtDNA D-loop of 251 Arabian horses to study the genetic diversity and phylogenetic relationships of Arabian populations and to examine the traditional strain classification system that depends on maternal family lines using native Arabian horses from the Middle East. Results: The variability in the upstream region of the D-loop revealed additional differences amo...
Marklund S, Ellegren H, Eriksson S, Sandberg K, Andersson L.Ten (TG)n positive clones, isolated from an equine genomic library and sequenced, contained 12-19 uninterrupted TG repeats. Primers for polymerase chain reaction (PCR) were synthesized and nine of these (TG)n loci (HTG7-15) were successfully amplified and utilized in this study together with five previously reported equine microsatellite loci (HTG2-6). The PCR products were analysed by polyacrylamide gel electrophoresis followed by automated laser fluorescence detection or autoradiography. All microsatellites showed polymorphism and stable Mendelian inheritance. Differences in microsatellite v...
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 ...
Swinburne JE, Boursnell M, Hill G, Pettitt L, Allen T, Chowdhary B, Hasegawa T, Kurosawa M, Leeb T, Mashima S, Mickelson JR, Raudsepp T, Tozaki T....A genetic linkage map of the horse consisting of 742 markers, which comprises a single linkage group for each of the autosomes and the X chromosome, is presented. The map has been generated from two three-generation full-sibling reference families, sired by the same stallion, in which there are 61 individuals in the F2 generation. Each linkage group has been assigned to a chromosome and oriented with reference to markers mapped by fluorescence in situ hybridization. The average interval between markers is 3.7 cM and the linkage groups collectively span 2772 cM. The 742 markers comprise 734 mic...
Bellone RR, Liu J, Petersen JL, Mack M, Singer-Berk M, Drögemüller C, Malvick J, Wallner B, Brem G, Penedo MC, Lassaline M.Squamous cell carcinoma (SCC) is the most common cancer of the equine eye, frequently originating at the limbus, with the potential to invade the cornea, cause visual impairment, and result in loss of the eye. Several breeds of horses have a high occurrence of limbal SCC implicating a genetic basis for limbal SCC predisposition. Pedigree analysis in the Haflinger breed supports a simple recessive mode of inheritance and a genome-wide association study (N = 23) identified a 1.5 Mb locus on ECA12 significantly associated with limbal SCC (Pcorrected = 0.04). Sequencing the most physiologicall...
