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Topic:Pedigree
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.
Genetic polymorphism of Hucul horse population based on 17 microsatellite loci. Short tandem repeat (STR) loci, i.e. microsatellites are a class of genetic markers commonly used for population studies and parentage control. This study determined the usefulness of microsatellite markers recommended by International Society for Animal Genetics (ISAG) for identification and pedigree analysis in horses based on the example of Polish Hucul horse population (Equus caballus). The set of seventeen microsatellites loci was tested (AHT4, AHT5, ASB2, HMS2, HMS3, HMS6, HMS7, HTG10, HTG4, HTG6, HTG7, VHL20, ASB17, ASB23, CA425, HMS1, LEX3) for 216 individuals. All samples were genotyp...
Inheritance of equine sarcoid disease in Franches-Montagnes horses. 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 ...
Maternal phylogenetic relationships and genetic variation among Arabian horse populations using whole mitochondrial DNA D-loop sequencing. 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...
Mitochondrial and pedigree analysis in Przewalski’s horse populations: implications for genetic management and reintroductions. Przewalski's horses have been imported from the western zoos to China since 1985. Yet the genetic diversity in China's populations has not been studied, thus lacking of such knowledge inevitably affects this population's management. The aim of this study was to assess genetic diversity in Chinese population of Przewalski's horses via mitochondrial DNA (mtDNA) control region and pedigree analysis. Methods: Two captive and one reintroduced populations were examined based on mitochondrial DNA control region variation via fecal sampling from 2010 to 2012, together with pedigree analysis. Results: ...
Genetic diversity and conservation in a small endangered horse population. The Old Kladruber horses arose in the 17th century as a breed used for ceremonial purposes. Currently, grey and black coat colour varieties exist as two sub-populations with different recent breeding history. As the population underwent historical bottlenecks and intensive inbreeding, loss of genetic variation is considered as the major threat. Therefore, genetic diversity in neutral and non-neutral molecular markers was examined in the current nucleus population. Fifty microsatellites, 13 single nucleotide polymorphisms (SNPs) in immunity-related genes, three mutations in coat colour genes an...
Genetic structure and gene flows within horses: a genealogical study at the french population scale. Since horse breeds constitute populations submitted to variable and multiple outcrossing events, we analyzed the genetic structure and gene flows considering horses raised in France. We used genealogical data, with a reference population of 547,620 horses born in France between 2002 and 2011, grouped according to 55 breed origins. On average, individuals had 6.3 equivalent generations known. Considering different population levels, fixation index decreased from an overall species FIT of 1.37%, to an average [Formula: see text] of -0.07% when considering the 55 origins, showing that most horse ...
Identification of genetic variation on the horse y chromosome and the tracing of male founder lineages in modern breeds. 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...
Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse. 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 ...
Implementation of Optimum Contributions selection in endangered local breeds: the case of the Menorca Horse population. Limiting the inbreeding rate (∆F) while maximizing genetic gain for any trait of economic interest is especially important in small populations of local breeds, like the Menorca Horse. In this breed, dressage performance is important for the profitability of the breed and should be accounted in the selection criterion. The aim of this study was to assess if a breeding programme aiming at improved dressage performance is feasible in such a small breed. To perform the analysis, animals that were currently available for breeding (between 3 and 20 years) were used. Selection was based on the es...
Computation of deregressed proofs for genomic selection when own phenotypes exist with an application in French show-jumping horses. 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...
Pedigree analysis and exclusion of alpha-tocopherol transfer protein (TTPA) as a candidate gene for neuroaxonal dystrophy in the American Quarter Horse. 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...
An integration of external information for foreign stallions into the Belgian genetic evaluation for jumping horses. The aim of this study was to test the integration of external information, i.e. foreign estimated breeding values (EBV) and the associated reliabilities (REL), for stallions into the Belgian genetic evaluation for jumping horses. The Belgian model is a bivariate repeatability Best Linear Unbiased Prediction animal model only based on Belgian performances, while Belgian breeders import horses from neighbouring countries. Hence, use of external information is needed as prior to achieve more accurate EBV. Pedigree and performance data contained 101382 horses and 712212 performances, respectively....
Ophthalmological findings in a closed herd of Lipizzaners. There are no studies on the ophthalmic health status in the Lipizzaner breed. Objective: To perform an ophthalmological survey in a closed herd in 3 housing systems. Methods: All horses at the Federal Stud Piber, Heldenberg and the Spanish Riding School Vienna were subjected to ophthalmological examination. Findings were documented and correlated with factors such as age, gender, location and housing situation. The interrelation of abnormalities of different regions was determined by calculating accuracy. Pedigree analysis of horses affected by cataract was performed. Results: A total of 267 h...
Thoroughbred racehorse mitochondrial DNA demonstrates closer than expected links between maternal genetic history and pedigree records. The potential future earnings and therefore value of Thoroughbred foals untested in the racing arena are calculated based on the performance of their forebears. Thus, lineage is of key importance. However, previous research indicates that maternally inherited mitochondrial DNA (mtDNA) does not correspond to maternal lineage according to recorded pedigree, casting doubt on the voracity of historic pedigrees. We analysed mtDNA of 296 Thoroughbred horses from 33 maternal lineages and identified an interesting trend. Subsequent to the founding of the Thoroughbred breed in the 16th century, well-po...
Pedigrees as a source of information in mtDNA studies of dogs and horses. The goal of this study was to demonstrate the usefulness of pedigree data in studies of mitochondrial DNA diversity in dogs and horses. Pedigree information allows for precisely choosing animals with distinct haplotypes for analysis, makes it possible to find rare haplotypes present exclusively in single individuals and helps to evaluate haplotype frequencies at the present and in the past. Estimating founder contributions to gene pools enables evaluating the parts of gene pools observed with the help of mtDNA analysis. An important aspect is also the financial benefits: using pedigree data, r...
Optimal contribution selection applied to the Norwegian and the North-Swedish cold-blooded trotter – a feasibility study. The aim of this study was to examine how to apply optimal contribution selection (OCS) in the Norwegian and the North-Swedish cold-blooded trotter and give practical recommendations for the future. OCS was implemented using the software Gencont with overlapping generations and selected a few, but young sires, as these turn over the generations faster and thus is less related to the mare candidates. In addition, a number of Swedish sires were selected as they were less related to the selection candidates. We concluded that implementing OCS is feasible to select sires (there is no selection on m...
Founder and present maternal diversity in two endangered Spanish horse breeds assessed via pedigree and mitochondrial DNA information. Pedigree information and 179 mtDNA sequences from two endangered Spanish horse breeds, the Asturcón pony (143) and the Mallorquí horse (36), were analysed to asses: (i) the pedigree and molecular maternal genetic diversity of the two breeds; (ii) the concordance between the dam lines recorded in the corresponding studbooks and the mtDNA haplotypes identified; and (iii) to assess the losses of maternal genetic variability occurred from the foundation of the studbooks to present. Up to 50 Asturcón and 18 Mallorquí founder dam lines were identified in the studbooks analysed. Up to 315 Asturc...
Genetic diversity and admixture among Canadian, Mountain and Moorland and Nordic pony populations. 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...
The genetic origin and history of speed in the Thoroughbred racehorse. 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...
Genetic structure and differentiation of the Italian catria horse. Catria is 1 of the 22 native Italian horse breeds that now survive from a larger number. Thirty individuals, representative of the Catria horse, were analyzed for 11 microsatellites and compared with data of 10 breeds reared in Italy. Three different approaches, genetic distances, correspondence analysis, and clustering methods, were considered to study genetic relationships among Catria and the other horse populations. Genetic differentiation among breeds was highly significant (P < 0.01) for all loci. Average F(ST) values indicate that around 10% of the total genetic variation was explain...
Equine degenerative myeloencephalopathy in Lusitano horses. Equine degenerative myeloencephalopathy (EDM) is a neurodegenerative disorder that has been previously associated with low vitamin E concentrations. Objective: To describe the clinical, electrophysiologic, and pathologic features of EDM in a group of related Lusitano horses. Methods: Fifteen Lusitano horses. Methods: Neurologic examinations were conducted, and serum vitamin E concentrations were measured. Three neurologically abnormal horses were further evaluated by ophthalmologic examination, electroretinography, electroencephalography, muscle and nerve biopsies, and post-mortem examination....
Phylogenetic relationships of the Hucul horse from Romania inferred from mitochondrial D-loop variation. 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...
Genetic stability in the Icelandic horse breed. Despite the Icelandic horse enjoying great popularity worldwide, the breed's gene pool is small. This is because of a millennium of isolation on Iceland, population crashes caused by natural disasters and selective breeding. Populations with small effective population sizes are considered to be more at risk of selection pressures such as disease and environmental change. By analysing historic and modern mitochondrial DNA sequences and nuclear coat colour genes, we examined real-time population dynamics in the Icelandic horse over the last 150 years. Despite the small gene pool of this breed, w...
Genetic characterization of the endangered Kiso horse using 31 microsatellite DNAs. 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...
Genetic analysis of Sicilian autochthonous horse breeds using nuclear and mitochondrial DNA markers. 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 ...
Inheritance of cerebellar abiotrophy in Arabians. To determine the mode of inheritance for cerebellar abiotrophy (CA), a neurologic disease in Arabians. Methods: 804 Arabians, including 29 horses (15 males and 14 females) with CA. Methods: Most horses (n = 755) belonged to 1 of 4 paternal families. Among the 29 CA-affected horses, all had clinical signs consistent with the disease; the disease was confirmed histologically following euthanasia in 8 horses. From the pedigree information, inbreeding coefficients were calculated for 16 affected horses and compared with coefficients for a subgroup of 16 unaffected horses. Complex segregation analy...
Validation of alternative models in genetic evaluation of racing performance in North Swedish and Norwegian cold-blooded trotters. There have been several approaches to the estimation of breeding values of performance in trotters, and the objective of this study was to validate different alternatives for genetic evaluation of racing performance in the North Swedish and Norwegian cold-blooded trotters. The current bivariate approach with the traits racing status (RACE) and earnings (EARN) was compared with a threshold-linear animal model and the univariate alternative with the performance trait only. The models were compared based on cross-validation of standardized earnings, using mean-squared errors of prediction (MSEP) ...
WorldFengur – the studbook of origin for the Icelandic horse. WorldFengur is the database that contains and functions as the studbook of origin of the Icelandic horse. Only pure-bred Icelandic horses, whose ancestry can be traced back to Iceland entirely, may be registered into WorldFengur. The WorldFengur project is a joint effort by the FAIC (Farmers Association of Iceland) and FEIF (International Federation of Icelandic Horse Associations) to construct an official and central database on horses of Icelandic origin located all over the world. It is used in this capacity in 19 countries so far; the number of data stored in the WorldFengur database has i...
Integrating databases for research on health and performance in small animals and horses in the Nordic countries. In a world of limited resources, using existing databases in research is a potentially cost-effective way to increase knowledge, given that correct and meaningful results are gained.Nordic examples of the use of secondary small animal and equine databases include studies based on data from tumour registries, breeding registries, young horse quality contest results, competition data, insurance databases, clinic data, prescription data and hunting ability tests. In spite of this extensive use of secondary databases, integration between databases is less common. The aim of this presentation is to...
Gametic phase disequilibrium between the syntenic multiallelic HTG4 and HMS3 markers widely used for parentage testing in Thoroughbred horses. Validation of parentage and horse breed registries through DNA typing relies on estimates of random match probabilities with DNA profiles generated from multiple polymorphic loci. Of the twenty-seven microsatellite loci recommended by the International Society for Animal Genetics for parentage testing in Thoroughbred horses, eleven are located on five chromosomes. An important aspect in determining combined exclusion probabilities is the ascertainment of the genetic linkage status of syntenic markers, which may affect reliable use of the product rule in estimating random match probabilities. I...
