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.
Perdomo-González DI, Laseca N, Demyda-Peyrás S, Valera M, Cervantes I, Molina A.Estimating inbreeding, which is omnipresent and inevitable in livestock populations, is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding. Inbreeding coefficients have been historically estimated by using pedigree information; however, over the last decade, genome-base inbreeding coefficients have come to the forefront in this field. The Pura Raza Española (PRE) horse is an autochthonous Spanish horse breed which has been recognised since 1912. The total PRE population (344,718 horses) was used to estimate C...
Kingsley NB, Sandmeyer L, Parker SE, Dwyer A, Heden S, Reilly C, Hallendar-Edman A, Archer S, Bellone RR.Equine recurrent uveitis (ERU) is the leading cause of blindness for horses; previous research implicated the leopard complex spotting allele (LP) as a genetic risk factor for insidious uveitis in the Appaloosa. There is limited information about risk in the Knabstrupper. Objective: To evaluate clinical manifestations, disease frequency and potential risk factors for ERU in Knabstrupper horses. Methods: Cross-sectional study. Methods: Ocular examinations were performed on 116 horses, and based on identified anomalies, horses were classified as suspect, ERU-affected or having no clinical signs....
Nolte W, Alkhoder H, Wobbe M, Stock KF, Kalm E, Vosgerau S, Krattenmacher N, Thaller G, Tetens J, Kühn C.In horses, parentage control is currently performed based on an internationally standardized panel of 17 microsatellite (MS) markers comprising 12 mandatory and five optional markers. Unlike MS, single nucleotide polymorphism (SNP) profiles support a wider portfolio of genomic applications, including parentage control. A transition to SNP-based parentage control is favorable, but requires additional efforts for ensuring generation-overlapping availability of marker genotypes of the same type. To avoid double genotyping of either parents or offspring for changing to SNP technology and enable ef...
Radovic L, Remer V, Krcal C, Rigler D, Brem G, Rayane A, Driss K, Benamar M, Machmoum M, Piro M, Krischke D, Butler-Wemken IV, Wallner B.In horses, demographic patterns are complex due to historical migrations and eventful breeding histories. Particularly puzzling is the ancestry of the North African horse, a founding horse breed, shaped by numerous influences throughout history. A genetic marker particularly suitable to investigate the paternal demographic history of populations is the non-recombining male-specific region of the Y chromosome (MSY). Using a recently established horse MSY haplotype (HT) topology and KASP™ genotyping, we illustrate MSY HT spectra of 119 Barb and Arab-Barb males, collected from the Maghreb regio...
Valberg SJ, Williams ZJ, Finno CJ, Schultz A, Velez-Irizarry D, Henry ML, Gardner K, Petersen JL.Both type 1 (PSSM1) and type 2 polysaccharide storage myopathy (PSSM2) are characterised by aggregates of abnormal polysaccharide in skeletal muscle. Whereas the genetic basis for PSSM1 is known (R309H GYS1), the cause of PSSM2 in Quarter Horses (PSSM2-QH) is unknown and glycogen concentrations not defined. Objective: To characterise the histopathological and biochemical features of PSSM2-QH and determine if an associated monogenic variant exists in genes known to cause glycogenosis. Methods: Retrospective case control. Methods: Sixty-four PSSM2-QH, 30 PSSM1-QH and 185 control-QH were identifi...
Perdomo-González DI, García de Paredes RLA, Valera M, Bartolomé E, Gómez MD.The studbook of Pura Raza Menorquina horses only permits the use of black-coated animals with a small quantity of white marks as breeding stock. Its breeding program uses linear morpho-functional traits as selection criteria. Our aim was to estimate the genetic parameters of linear morpho-functional traits, and reveal relationship of quality of black coat color (QB) and percentage of white marks (WM) with the other morphological and functional linear traits in this breed. A total of 46 linear traits were scored by four appraisers using seven classes, with a total of 772 records from 333 animal...
Possessing high meat and dairy productivity and good reproductive and adaptive qualities to year-round grazing, the Kushum breed plays an exceptional role in the improvement of productive qualities in horse herding in Kazakhstan and the former Soviet republics. The aim of the study was to develop breeding methods for creating new highly productive breeding lines for the Kushum breed horses. The leading method was linebreeding, which is based on the systematic use of remarkable animals, the offspring of which will accumulate and develop all the desired qualities and traits. The practical signif...
Kvist L, Honka J, Salazar D, Kirkinen T, Hemmann K.We used historical DNA samples to examine the history of a native horse breed, the Finnhorse. Samples were collected from private collections, museums, schools and excavations, representing the times prior to, during, and after the foundation of the breed; from the end of the 19th century and throughout the 20th century. We sequenced a fragment of mitochondrial DNA from these historical samples to study the history and evolution of maternal lineages of horses back to the early days of the breed, compared the mitochondrial DNA sequence diversity of different historical periods and modern day Fi...
Gmel AI, Burren A, Neuditschko M.Conformation traits such as joint angles are important selection criteria in equine breeding, but mainly consist of subjective evaluation scores given by breeding judges, showing limited variation. The horse shape space model extracts shape data from 246 landmarks (LM) and objective joint angle measurements from triplets of LM on standardized horse photographs. The heritability was estimated for 10 joint angles (seven were measured twice with different LM placements), and relative warp components of the whole shape, in 608 Franches-Montagnes (FM) horses (480 stallions, 68 mares and 60 geldings...
Klein R, Oláh J, Mihók S, Posta J.The Mezőhegyes Stud was founded in 1784 where three different horse breeds were developed: the Furioso-North Star, the Gidran, and the Nonius. These breeds were based on the same mare population, but each breed had different utilization purposes. Our aim was to analyze the pedigree information of these three indigenous breeds. The genealogical information was traced back from the actual breeding population back to the founder animals, and the final database contained more than 47,000 horses. The reference populations were defined as the registered breeding animals in 2019. The complete genera...
Myćka G, Klecel W, Stefaniuk-Szmukier M, Jaworska J, Musiał AD, Ropka-Molik K.The Polish draft horse (PDH) breed is a result of crossing local mares with imported cold-blooded stallions, such as Belgians, Ardennes, Fjords, and others. A part of the broodmare stock investigated in this study was also imported from various countries, such as Denmark. In this study, we investigate the genetic composition of the PDH by analyzing the whole mitochondrial d-loop variability and comparing it to previously demonstrated whole d-loop sequences of other cold-blooded breeds: Ardennais, Belgian, Breton, Clydesdale, Noriker, Norwegian Fjord, Percheron, and Suffolk. Our results show hi...
Hill EW, Stoffel MA, McGivney BA, MacHugh DE, Pemberton JM.Small effective population sizes and active inbreeding can lead to inbreeding depression due to deleterious recessive mutations exposed in the homozygous state. The Thoroughbred racehorse has low levels of population genetic diversity, but the effects of genomic inbreeding in the population are unknown. Here, we quantified inbreeding based on runs of homozygosity (ROH) using 297 K SNP genotypes from 6128 horses born in Europe and Australia, of which 13.2% were unraced. We show that a 10% increase in inbreeding () is associated with a 7% lower probability of ever racing. Moreover, a ROH-based g...
Bartolomé E, Valera M, Fernández J, Rodríguez-Ramilo ST.The equine breeding industry for sport's performance has evolved into a fairly profitable economic activity. In particular, the Caballo de Deporte Español (CDE) is bred for different disciplines with a special focus on Show Jumping. The main aim of this study was to determine the effects of 15 years of selection and to find out whether it has been effective and adequate regarding the CDE main breeding objectives. The whole pedigree of 19,045 horses registered as CDE was used, comprising 47,884 animals (18,799 males and 29,085 females). An analysis performed to check for the pedigree completen...
Wang M, Li H, Zhang X, Yang L, Liu Y, Liu S, Sun Y, Zhao C.The aim of the present study was to analyze the main factors that have a significant impact on skin thickness, and to further identify the genes and signaling pathways regulating skin growth by RNA-seq in Dezhou donkeys. Skin samples from different body regions of 15 slaughtered donkeys were obtained to study variations in skin thickness over the bodies. Skin thickness data for another 514 donkeys was obtained by minimally invasive skin sampling from the back, and measurements of the donkeys' body size traits and pedigree data were also collected. These data were used to analyze changes in ski...
Patterson Rosa L, Campos FA, Martin K, Vierra M, Foster G, Lundquist E, Brooks SA, Lafayette C.Pedigrees and horse written ancestry contain numerous inconsistencies and divergence between farm histories, owner accounts and registration records. In particular, the origins of the Brazilian Mangalarga, or "Mangalarga Paulista'' horse breed is controversial, and the breed's popular history claims that one of its most famous individuals, Turbante J.O., may have been sired by an unknown Hanoverian stallion. Turbante J.O. sired over 1678 offspring and is present in about 71% of the male pedigrees. We genotyped Turbante J.O. and 29 registered Mangalarga individuals using a commercially availabl...
Marín Navas C, Delgado Bermejo JV, McLean AK, León Jurado JM, Torres ARBYR, Navas González FJ.Genetic diversity and demographic parameters were computed to evaluate the historic effects of coat colour segregation in the process of configuration of the Hispano-Arabian horse (Há). Pedigree records from 207,100 individuals born between 1884 and 2019 were used. Although coat colour is not a determinant for the admission of Hispano-Arabian individuals as apt for breeding, it may provide a representative visual insight into the gene contribution of Spanish Purebred horses (PRE), given many of the dilution genes described in Há are not present in the Arabian Purebred breed (PRá). The lack ...
Remer V, Bozlak E, Felkel S, Radovic L, Rigler D, Grilz-Seger G, Stefaniuk-Szmukier M, Bugno-Poniewierska M, Brooks S, Miller DC, Antczak DF....The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian popul...
Lee J, Shin D, Kim H.Thoroughbred horses have been bred exclusively for racing in England for a long time. Additionally, because horse racing is a global sport, a healthy leisure activity for ordinary citizens, and a high-value business, systematic racehorse breeding at the population level is a requirement for continuous industrial development. Therefore, we established genomic evaluation system (using prize money as horse racing traits) to produce spirited, agile, and strong racing horse population. Methods: We used phenotypic data from 25,061 Thoroughbred horses (all registered individuals in Korea) that compet...
Cozzi MC, Valiati P, Longeri M, Ferreira C, Abreu Ferreira S.The Lusitano Horse (LH) originates from Portugal, but is reared worldwide. Since 1994, the University of Milan has routinely tested the LHs bred in Italy for parentage control. This study aims to assess the genetic variability of the LH reared in Italy using 16 microsatellites markers. Moreover, the genetic variability changes over the years in the total population (n.384) and in unrelated horses (n.47) were evaluated. Horses were grouped according to their date of birth (1975-1990, 1991-2000, 2001-2010, 2010-2019). Standard genetic diversity parameters, including observed (Ho) and expected (H...
The Journal of heredityDecember 12, 2021
Volume 113, Issue 3 238-247 doi: 10.1093/jhered/esab070
Esdaile E, Avila F, Bellone RR.American Standardbreds were developed as a harness racing horse breed. The United States Trotting Association closed the studbook in 1973 and implemented a book size cap in 2009. This study aimed to investigate genetic diversity in the American Standardbred after the studbook cap was introduced using short tandem repeats (STRs) and single-nucleotide polymorphisms (SNPs). Sixteen STRs from horses foaled from 2010 to 2015 and their sires and dams (n = 50 621) were utilized to examine allelic richness (Ar), expected heterozygosity (HE), observed heterozygosity (HO), unbiased heterozygosity (HU), ...
Perdomo-González DI, Molina A, Sánchez-Guerrero MJ, Bartolomé E, Varona L, Valera M.Fertility is a key factor in the economic success of horse farms. However, it has received little attention due to the difficulty of measuring fertility objectively. Since its studbook creation (1912), the Pura Raza Española (PRE) breed has been a closed population and become high in-bred resulting in inbreeding depression (poor phenotypic values). Nevertheless, heterogeneous effects of inbreeding depression have been detected among founders and nonfounders. The aims of this study were (1) to analyze the genetic parameters for reproductive traits in mares of the PRE horse breed and (2) to est...
Castaneda C, Juras R, Kjöllerström J, Hernandez Aviles C, Teague SR, Love CC, Cothran EG, Varner DD, Raudsepp T.This is a follow-up study to validate the previously detected association of the FKBP6 gene with stallion subfertility. Using a select cohort of 150 Thoroughbred stallions with detailed breeding records, we confirm significant association (P < 0.0001) between low per-cycle pregnancy rates (≤50%) and a combined A/A-A/A genotype of SNPs chr13:11 353 372G>A and chr13:11 353 436A>C in FKBP6 exon 5. We also show that stallion subfertility and the combined genotype A/A-A/A are not associated with the level of genetic diversity based on 12 autosomal microsatellite markers, or with pedig...
Dell A, Curry M, Hunter E, Dalton R, Yarnell K, Starbuck G, Wilson PB.The consequences of poor breed management and inbreeding can range from gradual declines in individual productivity to more serious fertility and mortality concerns. However, many small and closed groups, as well as larger unmanaged populations, are plagued by genetic regression, often due to a dearth in breeding support tools which are accessible and easy to use in supporting decision-making. To address this, we have developed a population management tool (BCAS, Breed Conservation and Management System) based on individual relatedness assessed using pedigree-based kinship, which offers breedi...
Park CS, Lee SY, Cho GJ.In this study, we aimed to investigate the recent changes such as allele frequencies and total probability of exclusion (PE) in Thoroughbred horses in Korea using short tandem repeat (STR) parentage panels between 2006 and 2016. Methods: The genotype was provided for 5,988 horse samples with 15 microsatellite markers (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3 and VHL20). Results: In our study, the observed number of alleles per locus ranged from 3 (HMS1) to 9 (ASB17) in 2006 and 4 (HMS1) to 9 (ASB2) in 2016, with a mean value of 6.28 and 6.40, respe...
Poyato-Bonilla J, Laseca N, Demyda-Peyrás S, Molina A, Valera M.The Carthusian horse is a Pura Raza Español (PRE) strain (CS), bred as a closed population since its creation more than 500 years ago. The aim of this study was to analyse for the first time its population structure and situation of variability combining both genealogical (GEL) and genomic (GEN) data. The GEL data comprised 348,429 pedigree records (56,105 CS horses), while the GEN analysis included the high-density genotypes (670,804 SNPs) of 287 horses. Pedigree completeness demonstrated its accuracy, showing a good correlation of GEL (F) and GEN (F ) inbreeding coefficient in the case of ...
Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Kusano K, Nagata SI.The Thoroughbred breed was formed by crossing Oriental horse breeds and British native horses and is currently used in horseracing worldwide. In this study, we constructed a single-nucleotide variant (SNV) database using data from 101 Thoroughbred racehorses. Whole genome sequencing (WGS) revealed 11,570,312 and 602,756 SNVs in autosomal (1-31) and X chromosomes, respectively, yielding a total of 12,173,068 SNVs. About 6.9% of identified SNVs were rare variants observed only in one allele in 101 horses. The number of SNVs detected in individual horses ranged from 4.8 to 5.3 million. Individual...
Shang S, Jiang R, Luo R, Jia S, Irwin DM, Wang Z, Zhang S.Individual identification of horses for pedigree verification and registration is important for the sustainable development of the horse industry. Horse individual identification and parentage tests commonly use the 17 short tandem repeats (STRs) recommended by the International Society for Animal Genetics (ISAG) and the locus LEX33. While many multiplex STR typing systems have been established for the horse, a sex determining marker is usually absent, and none of them can simultaneously detect all 17 ISAG recommended loci and the locus LEX33. Here, we present a 19-plex STR typing system that ...
Muñoz L, Donaire C, Salazar T, Ortiz R, Cruces J, Briones M.The Chilean horse is a breed of closed registry. Stall-walking and weaving are locomotor stereotypies that affect this breed, and genetic predisposition has been suggested for both conditions. The objective of the present study was to estimate heritability of stall-walking and weaving in Chilean horses. Owners of 2,098 horses registered in the Chilean horse Stud Book, which were or had been stabled for at least 1 year, were asked to provide for identification data of the animal and presence or absence of stall-walking and/or weaving. The Chilean Horse Stud Book was accessed online, to collect ...
Trachsel DS, Calloe K, Mykkänen AK, Raistakka P, Anttila M, Fredholm M, Tala M, Lamminpää K, Klaerke DA, Buhl R.Exercise-associated sudden deaths (EASDs) are deaths occurring unexpectedly during or immediately after exercise. Sudden cardiac death (SCD) is one cause of EASD. Cardiac arrhythmias caused by genetic variants have been linked to SCD in humans. We hypothesize that genetic variants may be associated with SCD in animals, including horses. Genetic variants are transmitted to offspring and their frequency might increase within a family. Therefore, the frequency of such variants might increase with the inbreeding factor. Higher inbreeding could have a negative impact on racing performance. Pedigree...
Mayhew IG, Watson AG, Heissan JA.From a clinical, radiological and morphological study of 9 horses with congenital malformations of the occiput, atlas and axis, and from a study of 2 reported cases, 3 diseases were defined: A. Familial occipitalisation of the atlas with atlantalisation of the axis in Arabian horses (7 cases in this report and the case reported by Leipold, et al., 1974). These horses had congenital atlantooccipital fusion, hypoplasia of the atlas and dens, malformation of the axis and modification of the atlantoaxial joint. B. Congenital asymmetrical occipitoatlantoaxial malformation (2 cases in this report). ...
Senju N, Tozaki T, Kakoi H, Shinjo A, Matsuyama R, Almunia J, Takasu M.Thirty-two microsatellites and a mitochondrial DNA haplotypes of endangered Yonaguni horses were analyzed to establish a pedigree registration system and to understand their genetic diversity for planning effective conservation. Blood samples were collected from 78 of the 130 horses in existence, and DNA was extracted and genotyped. There were two major findings. One is that it is possible to use microsatellites for Yonaguni horse pedigree registration in the future because the power of exclusion of parentage testing is reliable at 0.999998. The second is the clarification of the current genet...
Lopes MS, Mendonça D, Cymbron T, Valera M, da Costa-Ferreira J, Machado Ada C.The analysis of mitochondrial D-loop sequences (408 bp) from 145 Lusitano founder mares yielded a total of 27 different haplotypes. The distribution of these mtDNA sequences was quite unequal, with the three most frequent ones representing 56.5% of all the Lusitano founder mares and 14 haplotypes (51.9%) being rare variants found only once in the sampling. Four main haplotype clusters were present in the Lusitano breed. The comparison of these sequences with other equine haplotypes shows that they fall in groups shared with other horse breeds. These data support the hypothesis of multiple dome...
Wang M, Li H, Zhang X, Yang L, Liu Y, Liu S, Sun Y, Zhao C.The aim of the present study was to analyze the main factors that have a significant impact on skin thickness, and to further identify the genes and signaling pathways regulating skin growth by RNA-seq in Dezhou donkeys. Skin samples from different body regions of 15 slaughtered donkeys were obtained to study variations in skin thickness over the bodies. Skin thickness data for another 514 donkeys was obtained by minimally invasive skin sampling from the back, and measurements of the donkeys' body size traits and pedigree data were also collected. These data were used to analyze changes in ski...
Sandmeyer LS, Bellone RR, Archer S, Bauer BS, Nelson J, Forsyth G, Grahn BH. To determine if congenital stationary night blindness (CSNB) exists in the Miniature Horse in association with leopard complex spotting patterns (LP), and to investigate if CSNB in the Miniature Horse is associated with three single nucleotide polymorphisms (SNPs) in the region of TRPM1 that are highly associated with CSNB and LP in Appaloosas. Methods: Three groups of Miniature Horses were studied based on coat patterns suggestive of LP/LP (n=3), LP/lp (n=4), and lp/lp genotype (n=4). Methods: Horses were categorized based on phenotype as well as pedigree analysis as LP/LP, LP/lp,...
Mack M, Kowalski E, Grahn R, Bras D, Penedo MCT, Bellone R.A unique eye color, called tiger-eye, segregates in the Puerto Rican Paso Fino (PRPF) horse breed and is characterized by a bright yellow, amber, or orange iris. Pedigree analysis identified a simple autosomal recessive mode of inheritance for this trait. A genome-wide association study (GWAS) with 24 individuals identified a locus on ECA 1 reaching genome-wide significance ( = 1.32 × 10). This ECA1 locus harbors the candidate gene, (), (), with known roles in pigmentation in humans, mice, and zebrafish. Humans with compound heterozygous mutations in have oculocutaneous albinism (OCA) type...
Rieder S.Colour phenotypes may have played a major role during early domestication events and initial selection among domestic animal species. As coat colours mostly follow a relatively simple mode of Mendelian inheritance, they have been among the first traits to be systematically analysed at the molecular level. As a result of the number of genetic tools developed during the past decade, horse coat colour tests have been designed and are now commercially available for some of the basic phenotypes. These tests enable breeders to verify segregation within particular pedigrees, to select specific colour...
Poyato-Bonilla J, Perdomo-González DI, Sánchez-Guerrero MJ, Varona L, Molina A, Casellas J, Valera M.Inbreeding is caused by mating between related individuals and is associated with reduced fitness and performance (inbreeding depression). Several studies have detected heterogeneity in inbreeding depression among founder individuals. Recently, a procedure was developed to predict hidden inbreeding depression load that is associated with founders using the Mendelian sampling of non-founders. The objectives of this study were to: (1) analyse the population structure and general inbreeding, and (2) test this recent approach for predicting hidden inbreeding depression load for four morphological ...
Morgenthaler C, Diribarne M, Capitan A, Legendre R, Saintilan R, Gilles M, Esquerré D, Juras R, Khanshour A, Schibler L, Cothran G.Curly horses present a variety of curl phenotypes that are associated with various degrees of curliness of coat, mane, tail and ear hairs. Their origin is still a matter of debate and several genetic hypotheses have been formulated to explain the diversity in phenotype, including the combination of autosomal dominant and recessive alleles. Our purpose was to map the autosomal dominant curly hair locus and identify the causal variant using genome-wide association study (GWAS) and whole-genome sequencing approaches. Results: A GWAS was performed using a Bayesian sparse linear mixed model, based ...
Kavar T, Habe F, Brem G, Dovc P.Mitochondrial DNA from 49 Lipizzan horses representing 16 maternal lines from the original stud at Lipica was used for SSCP analysis and DNA sequencing. The SSCP analysis of the 444 bp long fragment of the D-loop region extending from the tRNA(Pro) gene to the central conserved sequence block revealed three distinct groups of SSCP patterns. Both ends of the D-loop region (378 bp and 310 bp), which are considered as the most variable regions within the mammalian mitochondrial DNA, were sequenced. According to 49 polymorphic sites identified within the both parts of the D-loop region, the 16 mat...
Christen G, Gerber V, Dolf G, Burger D, Koch C.The mode of inheritance for susceptibility to equine sarcoid disease (ES) remains unknown. The objectives of this study were to analyse a large sample of the Franches-Montagnes (FM) horse population and investigate the heritability and mode of inheritance for susceptibility to ES. Horses were clinically examined for the presence of sarcoid tumours. A standardized examination protocol and client questionnaire were used and a pedigree- and subsequent segregation-analysis for the ES trait performed. To investigate the mode of inheritance, five models were evaluated and compared in a hierarchical ...
Holl HM, Vanhnasy J, Everts RE, Hoefs-Martin K, Cook D, Brooks SA, Carpenter ML, Bustamante CD, Lafayette C.Genetic markers are important resources for individual identification and parentage assessment. Although short tandem repeats (STRs) have been the traditional DNA marker, technological advances have led to single nucleotide polymorphisms (SNPs) becoming an attractive alternative. SNPs can be highly multiplexed and automatically scored, which allows for easier standardization and sharing among laboratories. Equine parentage is currently assessed using STRs. We obtained a publicly available SNP dataset of 729 horses representing 32 diverse breeds. A proposed set of 101 SNPs was analyzed for DNA ...
Hill EW, Stoffel MA, McGivney BA, MacHugh DE, Pemberton JM.Small effective population sizes and active inbreeding can lead to inbreeding depression due to deleterious recessive mutations exposed in the homozygous state. The Thoroughbred racehorse has low levels of population genetic diversity, but the effects of genomic inbreeding in the population are unknown. Here, we quantified inbreeding based on runs of homozygosity (ROH) using 297 K SNP genotypes from 6128 horses born in Europe and Australia, of which 13.2% were unraced. We show that a 10% increase in inbreeding () is associated with a 7% lower probability of ever racing. Moreover, a ROH-based g...
A breed known for its versatility, the American Quarter Horse (QH), is increasingly bred for performance in specific disciplines. The impact of selective breeding on the diversity and structure of the QH breed was evaluated using pedigree analysis and genome-wide SNP data from horses representing 6 performance groups (halter, western pleasure, reining, working cow, cutting, and racing). Genotype data (36 037 single nucleotide polymorphisms [SNPs]) from 36 Thoroughbreds were also evaluated with those from the 132 performing QHs to evaluate the Thoroughbred's influence on QH diversity. Results s...
Luís C, Cothran EG, Oom Mdo M.The Sorraia horse is a closed breed with reduced effective population size and considered in critical maintained risk status. The breed exists in 2 main breeding populations, one in Portugal and one in Germany, with a smaller population size. A set of 22 microsatellite loci was used to examine genetic diversity and structure of the Sorraia horse breed and to compare individual inbreeding coefficient F, estimated from pedigree data, with individual heterozygosity and mean d(2). The Sorraia horse shows lower levels of microsatellite diversity when compared with other horse breeds. Due to managem...
Albertsdóttir E, Eriksson S, Sigurdsson Á, Árnason T.Genetic evaluation of Icelandic horses is currently based on results from breeding field tests where riding ability and conformation of the horses are evaluated over the course of 1-2 days. Only a small part of registered horses attend these field tests, and it can be assumed that these are not a random sample of the population. In this study, the trait test status was introduced, describing whether a horse was assessed in a breeding field test. This trait was analysed to find out whether it has a genetic variation and how it correlates genetically to other traits in the breeding goal. Breedin...
Sadeghi R, Moradi-Shahrbabak M, Miraei Ashtiani SR, Miller DC, Antczak DF.Previous research on the equine major histocompatibility complex (MHC) demonstrated strong correlations between haplotypes defined by polymorphic intra-MHC microsatellites and haplotypes defined using classical serology. Here, we estimated MHC diversity in a sample of 124 Arabian horses from an endangered strain native to Iran (Persian Asil Arabians), using a validated 10-marker microsatellite panel. In a group of 66 horses related as parent-offspring pairs or half-sibling groups, we defined 51 MHC haplotypes, 49 of which were new. In 47 of the remaining 58 unrelated horses, we could assign on...
Lassaline M, Cranford TL, Latimer CA, Bellone RR.To describe the prevalence of LSCC in Haflinger horses and to analyze affected horses' pedigrees investigating the genetic mode of inheritance. Methods: Fifteen horses met inclusion criterion of (i) being of the Haflinger breed, as confirmed by North American Haflinger Registry pedigree and (ii) being diagnosed with LSCC, as confirmed by clinical examination by a veterinary ophthalmologist or by histopathology. Pedigrees could not be obtained for four additional horses diagnosed with LSCC that had been identified as Haflingers. Methods: Retrospective medical record review of all 19 horses was ...
Beech J, Haskins M.A naturally occurring disease condition, neuraxonal dystrophy, was identified in 27 male and 15 female Morgans, many of which were closely related. Five-generation pedigrees were constructed for 33 of these horses and were compared with those for 29 randomly selected age- and sex-matched Morgans. Their mean coefficient of inbreeding was not statistically different (P greater than 0.1, 1 tailed t test; P less than 0.001, median test). Breeding of 2 severely affected and 2 normal stallions to 2 severely affected, 3 mildly affected, and 6 normal mares produced 10 mildly affected, 8 suspect affect...
Watson AG, Mayhew IG.Familial occipitalization of the atlas with atlantalization of the axis was defined as a single congenital disease in Arabian horses following a clinical, radiologic, and morphologic study of 16 horses with congenital malformations of the occiput, atlas, and axis, and from a study of three reported cases. The constant morphologic features were interpreted as congenital atlantooccipital fusion, hypoplasia of the atlas and dens, malformation of the axis, and modification of the atlantoaxial joint. Atlantoaxial subluxation was also a frequent finding. The clinical syndromes shown by these horses ...
Georgescu SE, Manea MA, Dudu A, Costache M.The existence of the Hucul horse on Romanian territory has been documented from the very distant past; today Hucul is a unique breed that is part of the FAO Program for the Preservation of Animal Genetic Resources. We compared Hucul with several primitive European and Asiatic breeds in order to elucidate the origin of these horses. We analyzed a 683-bp mitochondrial DNA (mtDNA) D-loop fragment in a population of Hucul horses and compared the polymorphic sites with sequences from other primitive breeds, including Exmoor, Icelandic Pony, Sorraia, Przewalski Horse, Mongolian Wild Horse, Konik, an...
Senju N, Tozaki T, Kakoi H, Almunia J, Maeda M, Matsuyama R, Takasu M.To help plan conservation of the endangered Miyako horse, a biological resource of the Miyako Islands in Japan, we characterized the genetics of the breed by genotyping 32 microsatellites and identifying mitochondrial DNA haplotypes. We also calculated genetic distances between individuals based on the proportion of shared alleles and visualized the genetic relationships with a phylogenetic tree. Two important results were obtained. One is that accurate pedigree registration of the horse by using microsatellites is possible, as the exclusion power of parentage testing is 0.999998. Another is t...
Prystupa JM, Juras R, Cothran EG, Buchanan FC, Plante Y.As part of the requirements of the Convention on Biological Diversity, Canada has been investigating the genetic diversity of its native equine and pony populations. Along with examining four indigenous Canadian equine populations (Canadian horse, Lac La Croix pony, Newfoundland pony and Sable Island population), another 10 Mountain and Moorland, three Nordic, four horse and two feral equine populations (thought to have influenced some pony breeds) were also investigated. In total, 821 individuals were genotyped at 38 microsatellite loci. Results of the analysis of molecular variance indicated...
Rudolph JA, Spier SJ, Byrns G, Hoffman EP.A genetic disease observed in certain Quarter horses is hyperkalaemic periodic paralysis (HYPP). This disease causes attacks of paralysis which can be induced by ingestion of potassium. Recent studies have shown that HYPP in humans is due to single base changes within the adult skeletal muscle sodium channel gene. A large Quarter horse pedigree segregating dominant HYPP was studied to determine if mutations of the sodium channel gene are similarly responsible for HYPP in horses. We used cross-species, PCR-mediated, cDNA cloning and sequencing of the horse adult skeletal muscle sodium channel a...
Ricard A, Danvy S, Legarra A.Genomic evaluations often use as pseudo-phenotypes corrected means of progeny performances, like daughter yield deviations (DYD) in dairy species. In horse breeding, own performances are also available and performances from other relatives (as half sibs) may play an important part in the EBV because the number of progeny remains low, even for stallions. The first step for genomic selection in horses is therefore to generate pseudo-phenotypes for genomic analysis when parental or own information is considered. This work presents an easy method to compute deregressed EBV from regular pedigree-ba...
Poncet PA, Pfister W, Muntwyler J, Glowatzki-Mullis ML, Gaillard C.Franches-Montagnes is the only native horse breed in Switzerland, therefore special efforts should be made for ensuring its survival. The objectives of this study were to characterize the structure of this population as well as genetic variability with pedigree data, conformation traits and molecular markers. Studies were focused to clarify if this population is composed of a heavy- and a light-type subpopulation. Extended pedigree records of 3-year-old stallions (n = 68) and mares (n = 108) were available. Evaluations of body conformation traits as well as pedigree data and molecular markers ...
Dimsoski P.To describe the development and performance of the new horse genotyping kit. Methods: Highly discriminatory 17-Plex horse genotyping kit was designed by adding the fifth dye to the StockMarks kit for genotyping horses and taking advantage of the new instrument platforms. This was accomplished by using a new set of five fluorescent dyes developed by Applied Biosystems (DS-31), with four of the dyes used to label the forward amplification primers (6-FAM, VIC, NED, and PET) in each primer set. Results: The new equine kit contained five extra loci (ASB17, LEX3, HMS1, CA425, and ASB23) in addition ...
Solé M, Valera M, Fernández J.The Pura Raza Español (PRE) is an autochthonous Spanish horse population distributed in 65 countries and managed by a single association. Since 1960s, breeding animals have been steadily exported to other countries to establish local subpopulations. We analysed the genetic structure of a PRE horse meta-population (MP) of 215,500 animals from countries with at least 80 active animals (27 countries comprising 77% of the total animals in the complete pedigree). Genotypes from active animals (59% of the total animals in the complete pedigree) were also studied. Genetic analysis of the MP was perf...
Sevinga M, Vrijenhoek T, Hesselinks JW, Barkema HW, Groen AF.This study was motivated by the hypothesis that the incidence of retained placenta (RP) in Friesian horses is associated with inbreeding. The objectives were to 1) calculate the inbreeding rate in the total registered Friesian horse population; 2) study the association of the inbreeding coefficient of the foal and the mare with the incidence of RP; and 3) study the heritability of RP in Friesian mares after normal foalings. Data from the total registered Friesian horse population from 1879 to 2000 (52,392 individuals) were collected from the registration files of the Friesian Horse Studbook. I...
The Journal of hereditySeptember 13, 2011
Volume 102, Issue 6 753-758 doi: 10.1093/jhered/esr091
Guastella AM, Zuccaro A, Criscione A, Marletta D, Bordonaro S.Genetic diversity and relationship among 3 Sicilian horse breeds were investigated using 16 microsatellite markers and a 397-bp length mitochondrial D-loop sequence. The analysis of autosomal DNA was performed on 191 horses (80 Siciliano [SIC], 61 Sanfratellano [SAN], and 50 Sicilian Oriental Purebred [SOP]). SIC and SAN breeds were notably higher in genetic variability than the SOP. Genetic distances and cluster analysis showed a close relationship between SIC and SAN breeds, as expected according to the breeds' history. Sequencing of hypervariable mitochondrial DNA region was performed on a ...
