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.
Głażewska I, Prusak B, Gralak B.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...
Olsen HF, Meuwissen T, Klemetsdal G.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...
Álvarez I, Fernández I, Lorenzo L, Payeras L, Cuervo M, Goyache F.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...
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...
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...
The Journal of heredityDecember 14, 2011
Volume 103, Issue 1 134-139 doi: 10.1093/jhered/esr121
Bigi D, Perrotta G.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...
Finno CJ, Higgins RJ, Aleman M, Ofri R, Hollingsworth SR, Bannasch DL, Reilly CM, Madigan JE.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....
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...
Campana MG, Stock F, Barrett E, Benecke N, Barker GW, Seetah K, Bower MA.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...
Takasu M, Hiramatsu N, Tozaki T, Kakoi H, Nakagawa T, Hasegawa T, Huricha , Maeda M, Murase T, Mukoyama H.In order to contribute to conservation of the endangered Kiso horse, we clarified their genetic information using 31 microsatellite DNAs, and genotyped 125 horses, 83% of the existing breed. First, we clarified the current status of the horses. The horses were confirmed to have experienced rapid loss of population causing a bottleneck, and their effective population size was much smaller than their census size. Moreover, the number of alleles (6.3), observed heterozygosity (0.674), and expected heterozygosity (0.662) were in the same range as other endangered horses all over the world. Therefo...
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 ...
Brault LS, Famula TR, Penedo MC.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...
Olsen HF, Klemetsdal G, Odegård J, Arnason T.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) ...
Lorange JB.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...
Egenvall A, Nødtvedt A, Roepstorff L, Bonnett B.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...
Machado FB, de Vasconcellos Machado L, Bydlowski CR, Bydlowski SP, Medina-Acosta E.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...
Hasler H, Flury C, Menet S, Haase B, Leeb T, Simianer H, Poncet PA, Rieder S.The Franches-Montagnes is an indigenous Swiss horse breed, with approximately 2500 foalings per year. The stud book is closed, and no introgression from other horse breeds was conducted since 1998. Since 2006, breeding values for 43 different traits (conformation, performance and coat colour) are estimated with a best linear unbiased prediction (BLUP) multiple trait animal model. In this study, we evaluated the genetic diversity for the breeding population, considering the years from 2003 to 2008. Only horses with at least one progeny during that time span were included. Results were obtained ...
Mari G, Castagnetti C, Rizzato G, Mislei B, Iacono E, Merlo B.Stallions are not selected for fertility but for other criteria (pedigree, conformation, performances, progeny), therefore valuable but subfertile stallions with poor semen quality are frequently used in commercial breeding programs. The object of this study was to evaluate whether sperm selection through a silane-coated silica colloid gradient centrifugation, with or without the addition of seminal plasma of a high fertile stallion, could improve the pregnancy rates of an oligospermic valuable stallion in a commercial breeding program. In 2008 breeding season (experiment 1, n=104 mares), simp...
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,...
van de Goor LH, van Haeringen WA, Lenstra JA.As a consequence of the close integration of horses into human society, equine DNA analysis has become relevant for forensic purposes. However, the information content of the equine Short Tandem Repeat (STR) loci commonly used for the identification or paternity testing has so far not been fully characterized. Population studies were performed for 17 polymorphic STR loci (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10, LEX3 and VHL20) including 8641 horses representing 35 populations. The power of parental exclusion, polymorphic information content...
Brault LS, Penedo MC.A putative mutation causative of cerebellar abiotrophy (CA), a genetic defect found almost exclusively in Arabian horses, was recently identified. Objective: To investigate the presence of the CA mutation in breeds other than Arabian and ascertain whether the mutation had been introduced into these breeds by Arabian ancestry. The CA mutation is present in breeds of horses with Arabian ancestry. Methods: Allele-specific PCR was used to genotype 1845 non-Arabian horses for the CA mutation. For those breeds in which at least one carrier was identified, an additional 266 horses were genotyped to d...
Pinard CL, Basrur PK.To characterize the ocular anomalies, determine their recurrence in families and assess the mode of inheritance of the most prevalent anomalies through pedigree analysis in a herd of Exmoor ponies. Methods: Thirty Exmoor ponies residing in south-western Ontario, Canada. Methods: Ophthalmic examination was performed using direct ophthalmoscopy, slit-lamp biomicroscopy and indirect ophthalmoscopy, pre- and post-pupillary dilation. Following compilation of ocular findings, pedigree analysis was conducted to assess the recurrence pattern of specific anomalies in families and the data were tested f...
Bömcke E, Gengler N, Cothran EG.In Greece, seven native horse breeds have been identified so far. Among these, the Skyros pony is outstanding through having a distinct phenotype. In the present study, the aim was to assess genetic diversity in this breed, by using different types of genetic loci and available genealogical information. Its relationships with the other Greek, as well as foreign, domestic breeds were also investigated. Through microsatellite and pedigree analysis it appeared that the Skyros presented a similar level of genetic diversity to the other European breeds. Nevertheless, comparisons between DNA-based a...
Goyache F, Alvarez I, Fernández I, Pérez-Pardal L, Royo LJ, Lorenzo L.Empirical evidence of the usefulness of different molecular-based methods to estimate the effective population size (N(e)) for conservation purposes in endangered livestock populations is reported. The black-coated Asturcón pony pedigree (1,981 individuals) was available. Additionally, a total of 267 Asturcón individuals born in 1998, 2002, and 2008 were typed for 15 microsatellites. These yearly cohorts (cohort(1998, 2002, 2008)) included almost all individuals kept for reproduction at the end of the corresponding foaling season. The genealogical realized N(e) was estimated for each cohort ...
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...
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...
Campana MG, Whitten CM, Edwards CJ, Stock F, Murphy AM, Binns MM, Barker GW, Bower MA.Historic DNA data have the potential to identify phenotypic information otherwise invisible in the historical, archaeological and palaeontological record. In order to determine whether a single nucleotide polymorphism typing protocol based on single based extension (SNaPshot™) could produce reliable phenotypic data from historic samples, we genotyped three coat colour markers for a sample of historic Thoroughbred horses for which both phenotypic and correct genotypic information were known from pedigree information in the General Stud Book. Experimental results were consistent with the pedig...
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...
Bömcke E, Soyeurt H, Szydlowski M, Gengler N.Relationship coefficients are traditionally based on pedigree data. Today, with the development of molecular techniques, they are often completely replaced by coefficients calculated from molecular data. Examples are relationships from microsatellites for biodiversity studies but also genomic relationships from SNP as currently used in genomic prediction of breeding values. There are, however, many situations in which optimal combination of both sources would be the best solutions. Obviously, this is the case for incompletely genotyped populations, but also when pedigree information is sparse....
Yamashita J, Oki H, Hasegawa T, Honda T, Nomura T.Genetic contributions of nine historically important ancestors and allelic diversity in the Japanese Thoroughbred population were examined by applying the gene dropping simulation to the foals produced from 1978 to 2005. Full pedigree records traced to ancestors (base animals) born around 1890 were used for the simulation. Alleles originated from some of the historically important ancestors were found to be at risk of future extinction, although their genetic contributions to the foal population have increased during the last three decades. The proportion of surviving alleles to the total alle...
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...
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...
The Journal of heredityMay 1, 1994
Volume 85, Issue 3 222-224 doi: 10.1093/oxfordjournals.jhered.a111439
Bowling AT.Analysis of selected studbook records of the American Paint Horse Association, consisting of 687 foals sired by 13 overo stallions from non-overo mares, supports the inheritance of overo spotting as an autosomal dominant gene. More than one gene may control patterns registered as overo. Additional studies are necessary to explain the sporadic occurrence of overo spotting from nonspotted quarter horse parents and to confirm the inheritance of overo spotting in other breeds.
Aberle K, Wrede J, Distl O.We analysed the relationship coefficients (R) between the four German heavy horse breeds South German Coldblood, Rhenish German Draught Horse, Schleswig Draught Horse and Black Forest Draught Horse. The relationship coefficient makes it possible to ascertain crossbreeding between the breeds over time, or autonomous developments of the breeds, respectively. The investigation revealed that the relationship coefficients between the German draught horse breeds were very low. The mean relationship coefficients between the four German heavy horse breeds were largest between the South German Coldbloo...
Lorange JB.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...
Ojala M, Ala-Huikku J.From 1974 to 1979, seven stillborn foals with internal hydrocephalus were encountered from one Standardbred trotter stallion which sired 239 registered foals. An hydrocephalic foal was also aborted by a daughter of the same stallion. One affected foal from Standardbred trotters and one from a Finnish Horses were also reported. In some cases, the condition caused severe dystocia. Based on field data, possible causes of the defect could neither be proved nor specifically overruled in individual cases. Hydrocephalus was obviously not an autosomal recessive single-locus defect, nor was it X-linked...
Kent MG, Shoffner RN, Buoen L, Weber AF.The XY sex-reversal syndrome occurs when a phenotypic mare is born that has the karyotype of a stallion. The syndrome is manifested by both genotypic and phenotypic heterogeneity. The sex-reversed genetic condition occurs frequently within certain pedigrees where XY females have been found and can be readily detected by chromosome karyotyping. The phenotypic spectrum ranges from the feminine mare with a reproductive tract that is within normal limits to the greatly masculinized mare. Pedigree analysis suggests that there are two modes of inheritance: (1) an X-linked recessive or autosomal sex-...
Fornal A, Radko A, Piestrzyńska-Kajtoch A.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...
Rivas VN, Magdesian KG, Fagan S, Slovis NM, Luethy D, Javsicas LH, Caserto BG, Miller AD, Dahlgren AR, Peterson J, Hales EN, Peng S, Watson KD....Idiopathic hypocalcemia in Thoroughbred (TB) foals causes tetany and seizures and is invariably fatal. Based upon the similarity of this disease with human familial hypoparathyroidism and occurrence only in the TB breed, we conducted a genetic investigation on two affected TB foals. Familial hypoparathyroidism was identified, and pedigree analysis suggested an autosomal recessive (AR) mode of inheritance. We performed whole-genome sequencing of the two foals, their unaffected dams and four unaffected, unrelated TB horses. Both homozygosity mapping and an association analysis were used to prior...
Kelly L, Postiglioni A, De Andrés DF, Vega-Plá JL, Gagliardi R, Biagetti R, Franco J.The genetic variability within the Uruguayan Creole horse and its relationship to a group of geographically or historically related breeds (Spanish Pure-bred, Barb, Quarter horse, Paso Fino, Peruvian Paso, Arabian and Thoroughbred horse), was evaluated using 25 loci (seven of blood groups, nine of protein polymorphisms and nine microsatellites) analyzed on a total of 145 Uruguayan Creole horses. In this study, blood group and protein polymorphism variants that are considered to be breed markers of Spanish Pure-bred and Barb horses were detected in the Creole breed. Conversely, some microsatell...
Luís C, Bastos-Silveira C, Costa-Ferreira J, Cothran EG, Oom MM.A common female founder individual of the Portuguese horse breeds Sorraia and Lusitano was found while conducting research on the variation of the Lusitano mitochondrial DNA lineages in relation to studbook information. We obtained 416-bp control region sequences from 16 descendents of a female Sorraia founder (Pomba) still represented in the living population of the Lusitano, according to the most recent edition of this breed's studbook. The same haplotype was found for all analysed samples and belongs to the haplogroup described by several authors as having predominantly Iberian, South Ameri...
Bomcke E, Gengler N.Relationship coefficients are particularly useful to improve genetic management of endangered populations. These coefficients are traditionally based on pedigree data, but in case of incomplete or inexistent pedigrees they are replaced by coefficients calculated from molecular data. The main objective of this study was to develop a new method to estimate relationship coefficients by combining molecular with pedigree data, which is useful for specific situations where neither pedigree nor molecular data are complete. The developed method was applied to contribute to the conservation of the Skyr...
Weideman H, Schoeman SJ, Jordaan GF.This study was carried out to estimate the heritability of liability to epistaxis in the southern African Thoroughbred population. Data of all horses that suffered epistaxis while racing in southern Africa and Mauritius from 1986 to 2002 and involving 1252 bleeders were analysed. Pedigree data covering the period 1960-1986 was used as required to calculate the incidence of bleeding amongst ancestors of the post-1986 era. Only pedigrees of horses that raced were included in this study as it was not possible to predict whether non-runners would have bled had they raced. Consequently all non-runn...
Silva AP, Curi RA, Langlois B, Silva JA.In this study, we estimated the heritability (h(2)) of earnings in the Quarter Horse in order to evaluate the inclusion of this trait in breeding programs. Records from 14,754 races of 2443 horses from 1978-2009 were provided by Sorocaba Hippodrome, São Paulo, Brazil. All ancestors of the registered horses were included in the pedigree file until the 4th generation. Log-transformed performance measures (LPM) were analyzed for animals aged 2, 3, and 4 years and during their entire career. The h(2) estimates were obtained using a multi-trait model and Gibbs sampling that included the effects of...
Yahagi Rodrigues L, da Silva Faria RA, de Vasconcelos Silva JAI.The aim of this study was to evaluate the genetic diversity and to identify the most influential ancestors in the population of Brazilian Quarter Horses participating in cutting competitions. Data from 1,590 elite horses born between 1970 and 2015, which participated in cutting competitions between 1981 and 2018, were evaluated based on the pedigree file that contained 5,832 animals born since 1834. Evaluation of the quality of the pedigree data showed a mean number of known equivalent generations of 5.4 ± 1.5 and a mean generation interval of 11.7 ± 8.8 years. The inbreeding coefficient (1...
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...
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 ...
Haechler S, Van den Ingh TS, Rogivue C, Ehrensperger F, Welle M.Congenital hepatic fibrosis with autosomal recessive or dominant inheritance has been described in humans, cats, piglets, and dogs. In horses, only two cases of congenital hepatic fibrosis have been previously reported. This retrospective study of records from the Institute for Animal Pathology, University of Berne, identified 30 foals with liver lesions compatible with congenital hepatic fibrosis. Anamnestic data revealed clinical signs of severe liver injury in most affected animals. Pathologic examination showed severely enlarged, firm livers with thin-walled cysts. Histologically, the live...
Poyato-Bonilla J, Sánchez-Guerrero MJ, Cervantes I, Gutiérrez JP, Valera M.Measurements from 13 different morphological traits of importance in the Pura Raza Español (PRE) horse were used to estimate genetic and environmental parameters following a heteroscedastic model in which data were assigned to stallions. Data sets used ranged from 20,610 (height at withers) to 48,486 measurements (length of shoulder), and the number of animals analysed in the pedigrees varied from 17,662 (height at withers) to 23,962 (dorsal-sternal diameter). Results of heritabilities of the traits varied from 0.09 (width of chest and upper neck line) to 0.30 (muscular development). Further,...
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...
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...
Ricard A, Crevier-Denoix N, Pourcelot P, Crichan H, Sabbagh M, Dumont-Saint-Priest B, Danvy S.For centuries, morphology has been the most commonly selected trait in horses. A 3D video recording enabled us to obtain the coordinates of 43 anatomical landmarks of 2089 jumping horses. Generalized Procrustes analysis provided centered and scaled coordinates that were independent of volume, i.e., centroid size. Genetic analysis of these coordinates (mixed model; 17,994 horses in the pedigree) allowed us to estimate a variance-covariance matrix. New phenotypes were then defined: the "summarized shapes". They were obtained by linear combinations of Procrustes coordinates with, as coefficients,...
Rubin CJ, Hodge M, Naboulsi R, Beckman M, Bellone RR, Kallenberg A, J'Usrey S, Ohmura H, Seki K, Furukawa R, Ohnuma A, Davis BW, Tozaki T, Lindgren G....The Greying with age phenotype in horses involves loss of hair pigmentation whereas skin pigmentation is not reduced, and a predisposition to melanoma. The causal mutation was initially reported as a duplication of a 4.6 kb intronic sequence in Syntaxin 17. The speed of greying varies considerably among Grey horses. Here we demonstrate the presence of two different Grey alleles, G2 carrying two tandem copies of the duplicated sequence and G3 carrying three. The latter is by far the most common allele, probably due to strong selection for the striking white phenotype. Our results reveal a rem...
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 ...
Dang W, Shang S, Zhang X, Yu Y, Irwin DM, Wang Z, Zhang S.Previous studies investigating donkey parentage and genetic diversity used horse-specific multiplex systems. However, several mis-allele and null-allele issues were found with some of the horse primers when used in donkeys. In 2017, the International Society for Animal Genetics (ISAG) recommended 13 dinucleotide short tandem repeats (STRs) (AHT4, ASB23, HMS2, HMS3, HMS6, HMS7, HMS18, HTG7, HTG10, TKY297, TKY312, TKY337 and TKY343) as a core panel that should be used to identify individuals and to test for parentage in donkeys. To date, no single multiplex STR typing system containing all 13 do...
Kaminski M, de Andres Cara DF.Genetic variants at eight blood loci were analysed, disclosing in Andalusian breed six rare markers: variants J of transferrin, H of esterase, D and S of Xk, M and W of prealbumin. Two of these, TfJ and PrM appear as characteristic markers of Andalusian breed. Allelic frequencies showed minor differences between Spanish (300 horses) and Lusitanian (100 horses) populations. Comparison was established with historically related breeds, Thoroughbreds or Connemara, and with Arab horses because of a presumed relationship. No visible similarities in genetic profiles were found with two former breeds,...
