Inbreeding in horses refers to the mating of individuals that are closely related genetically, resulting in offspring with a higher degree of genetic similarity. This practice can lead to an increased risk of homozygosity for deleterious alleles, which may affect health, performance, and reproductive traits. Inbreeding is often measured by the inbreeding coefficient, which quantifies the probability that two alleles at a locus are identical by descent. While inbreeding can consolidate desirable traits within a breed, it may also reduce genetic diversity and increase the likelihood of inherited disorders. This page compiles peer-reviewed research studies and scholarly articles that explore the genetic, physiological, and health implications of inbreeding in equine populations.
Fröhlich DE, Wallner B, Juras R, Cothran EG, Velie BD.Timor ponies (TP) were first shipped to Australia in the early 1800s and were highly valued as transport and pack animals, which resulted in TPs contributing to the development of Australian horse breeds. Today, while the exact number of TPs in Australia is currently unknown, there has been recent interest in establishing a domestic breeding program for Australian TPs. The aim of this study was to evaluate the relatedness of a sample of TPs, as well as provide estimates of genomic inbreeding levels to better inform the feasibility of using these animals as founders for a domestic breeding prog...
Lawson JM, Shilton CA, Lindsay-McGee V, Psifidi A, Wathes DC, Raudsepp T, de Mestre AM.Excessive inbreeding increases the probability of uncovering homozygous recessive genotypes and has been associated with an increased risk of retained placenta and lower semen quality. No genomic analysis has investigated the association between inbreeding levels and pregnancy loss. Objective: To compare genetic inbreeding coefficients (F) of naturally occurring Thoroughbred Early Pregnancy Loss (EPLs), Mid and Late term Pregnancy Loss (MLPL) and Controls. The F value was hypothesised to be higher in cases of pregnancy loss (EPLs and MLPLs) than Controls. Methods: Observational case-control st...
Atroshchenko M, Dementieva N, Shcherbakov Y, Nikolaeva O, Azovtseva A, Ryabova A, Nikitkina E, Makhmutova O, Datsyshin A, Zakharov V, Zaitsev A.Horses were domesticated later than other farm animals. Horse breeds have been selectively developed by humans to satisfy different needs and purposes. The factory and indigenous breeds are of particular interest, having been bred in purity for many centuries without the addition of foreign blood. Data from 31 stud farms, as well as ranches, located in fifteen regions of the Russian Federation were used in this work. DNA was sampled from 102 stallions of 11 breeds: Arabian, Akhal-Teke, Don, Orlov Trotter, Vladimir Heavy Draft, Russian Heavy Draft, Soviet Heavy Draft, Kabardin, Yakut, Tuva, and...
Berglund P, Andonov S, Strandberg E, Eriksson S.Speed, in the form of racing time per kilometre (km), is a performance trait of the Swedish-Norwegian Coldblooded trotter included in the joint Swedish-Norwegian genetic evaluation. A few popular stallions have dominated Coldblooded trotter breeding, which has led to an increasing average relationship between individuals in the population. This study investigated the scope for broadening the breeding goal by selecting for racing time per km over different race lengths (short: 1640 m, medium: 2140 m and long: 2640 m), as this could encourage the use of breeding sires that are less related...
Ripollés-Lobo M, Perdomo-González DI, Azor PJ, Valera M.Abnormalities in hoof shape are usually connected with limb conformation defects. The role of angular hoof deviations is important for longevity in sports competitions and is increasingly recognized as a factor associated with lameness in performance horses. In this paper, we measured the prevalence of four defects related to the angulation of the hoof in the Pura Raza Española horse (PRE): splay-footed forelimb (SFF), pigeon-toed forelimb (PTF), splay-footed rear limb (SFR), and pigeon-toed rear limb (PTR). A total of 51,134 animals were studied, of which only 15.75% did not have any of the ...
Zimmermann E, Ros KB, Pfarrer C, Distl O.Malformations of the equine cervicothoracic junction affect the C6 and C7 cervical vertebrae, the T1 thoracic vertebra and in variable extent the first and second sternal ribs. To date, the clinical impact of this malformation, its prevalence and mode of inheritance in equine populations are not yet determined. We examined five skeletons for signs of malformation of the cervicothoracic junction, including three skeletons from widely used Thoroughbred stallions affected with the malformation and two skeletons serving as a comparison. The three affected historical horses were the Thoroughbred st...
Encina A, Ligero M, Sánchez-Guerrero MJ, Rodríguez-Sainz de Los Terreros A, Bartolomé E, Valera M.Hair whorls are a hereditary feature in horses that may be associated with temperament and coat color. Hair whorls are described as changes in the hair pattern and may take various forms, such as circular and linear whorls. We first carried out a frequency analysis of hair whorls (circular and linear). Next, a Generalized Non-Linear Model was computed to assess the significance of some potential influencing factors, and a genetic parameter estimation was performed. ENDOG software v4.8 was used to estimate the inbreeding coefficient of all the animals analyzed. It was more common to find horses...
Sohail Ashraf M, Basheer A, Iqbal F, Zahoor I.The current study aimed to evaluate the genetic diversity, level of admixture, and phylogenetic relationship, of the Pakistani horse breeds, along with their morphological characterization. Data for the body measurements showed that Morna horses had the highest values of body height, body length, chest girth, leg length, and head length, whereas the Baluchi horses had the lowest values for these traits. For the genetic diversity 64 animals, 15/breed except for Baluchi(14) and Topras(05), were genotyped by using the 17-plex equine genotyping kit. The AMOVA results showed that 13% of genetic div...
Lindsay-McGee V, Sanchez-Molano E, Banos G, Clark EL, Piercy RJ, Psifidi A.The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of th...
Bhardwaj A, Tandon G, Pal Y, Sharma NK, Nayan V, Soni S, Iquebal MA, Jaiswal S, Legha RA, Talluri TR, Bhattacharya TK, Kumar D, Rai A, Tripathi BN.The horse, one of the most domesticated animals, has been used for several purposes, like transportation, hunting, in sport, or for agriculture-related works. Kathiawari, Marwari, Manipuri, Zanskari, Bhutia, Spiti, and Thoroughbred are the main breeds of horses, particularly due to their agroclimatic adaptation and role in any kind of strong physical activity, and these characteristics are majorly governed by genetic factors. The genetic diversity and phylogenetic relationship of these Indian equine breeds using microsatellite markers have been reported, but further studies exploring the SNP d...
Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Nagata SI.Individual identification and paternity testing are important for avoiding inbreeding in the management of small populations of wild and domestic animals. In horse racing industries, they are extremely important for identifying and registering individuals and doping control to ensure fair competition. In this study, we constructed an individual identification panel for horses by using insertion and deletion (INDEL) markers. The panel included 39 INDEL markers selected from a whole-genome INDEL database. Genotyping of 89 Thoroughbreds showed polymorphisms with minor allele frequencies (MAFs) of...
Dementieva N, Nikitkina E, Shcherbakov Y, Nikolaeva O, Mitrofanova O, Ryabova A, Atroshchenko M, Makhmutova O, Zaitsev A.The specifics of breeding and selection significantly affect genetic diversity and variability within a breed. We present the data obtained from the genetic analysis of 21 thoroughbred and warmblood horse breeds. The most detailed information is described from the following breeds: Arabian, Trakehner, French Trotter, Standardbred, and Soviet Heavy Horse. The analysis of 509,617 SNP variants in 87 stallions from 21 populations made it possible to estimate the genetic diversity at the genome-wide level and distinguish the studied horse breeds from each other. In this study, we searched for heter...
Todd ET, Fromentier A, Sutcliffe R, Running Horse Collin Y, Perdereau A, Aury JM, Èche C, Bouchez O, Donnadieu C, Wincker P, Kalbfleisch T....Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski's horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with high...
Santos WB, Pereira CB, Maiorano AM, Arce CDS, Baldassini WA, Pereira GL, Chardulo LAL, Neto ORM, Oliveira HN, Curi RA.With the advent of genomics, significant progress has been made in the genetic improvement of livestock species, particularly through increased accuracy in predicting breeding values for selecting superior animals and the possibility of performing a high-resolution genetic scan throughout the genome of an individual. The main objectives of this study were to estimate the individual genomic inbreeding coefficient based on runs of homozygosity (F ), to identify and characterize runs of homozygosity and heterozygosity (ROH and ROHet, respectively; length and distribution) throughout the genome, a...
Chen C, Zhu B, Tang X, Chen B, Liu M, Gao N, Li S, Gu J.In the genomes of diploid organisms, runs of homozygosity (ROH), consecutive segments of homozygosity, are extended. ROH can be applied to evaluate the inbreeding situation of individuals without pedigree data and to detect selective signatures via ROH islands. We sequenced and analyzed data derived from the whole-genome sequencing of 97 horses, investigated the distribution of genome-wide ROH patterns, and calculated ROH-based inbreeding coefficients for 16 representative horse varieties from around the world. Our findings indicated that both ancient and recent inbreeding occurrences had vary...
Gonçalves AR, Telo da Gama L, Antunes L, Guimarães H, Bliebernicht M, Duarte JC, Cosinha C, Duarte Rego B, Ferro da Costa P, Guimarães T, Rocha A....The objectives of this study were to establish baseline information for seminal traits in Lusitano stallions, to assess the impact of inbreeding, interval between collections and age on semen quality during the breeding and non-breeding seasons, and to estimate the corresponding genetic parameters. A total of 2129 ejaculates by 146 Lusitano stallions used for artificial insemination, obtained from four equine reproduction centers distributed throughout Portugal, over a period of 14 years (2008-2021), were included in the study. The seminal traits analyzed, and the corresponding means and stand...
Masuda M, Nikadori A, Nikadori E, Uchida N, Takizawa Y, Ishimaru M, Yamamoto T, Yuasa R, Kugai H, Nagahama Y, Takasu M, Tozaki T.The Miyako horse is a native Japanese horse breed. As with other native Japanese horses, the number of Miyako horses decreased due to mechanization and motorization, which reduced their roles, with just 14 in 1980. Although their population had increased to 55 horses by 2021, a further increase in their numbers is required to avoid extinction. Recently, their breeding has involved natural mating during group grazing; therefore, pedigree management has been difficult, and individual identification has been inconclusive. With the aim of formulating an effective breeding plan, this study used mic...
Hill EW, McGivney BA, MacHugh DE.The proportion of the genome containing runs of homozygosity (ROH) affects production traits in livestock populations. In European and Australasian Thoroughbreds inbreeding, quantified using ROH (F ), is associated with the probability of ever racing. Here, we measured F using 333 K SNP genotypes from 768 Thoroughbred horses born in North America to evaluate the effect of inbreeding on racing traits in that region. Among North American horses, F was not associated (p = 0.518) with the probability of ever racing but was significantly associated with the number of race starts (p = 0.002). ...
Yoshihara T, Kikuchi M, Akiba Y, Horiguchi M, Takasu M, Tozaki T.The Taishu horse in Tsushima is one of eight Japanese native breeds. The breed is on the verge of extinction due to a rapid decrease in numbers since the 1960s owing to motorization in Japan. In this study, we aimed to confirm the pedigree information of 52 horses by genotyping 31 microsatellites in order to avoid inbreeding. Parentage verification failed to identify genetic contradictions among trios (sires, dams, and foals) registered with the Japan Equine Affairs Association (JEAA). Pedigree information registered at the JEAA was obtained and adequately understood. Additionally, the genetic...
Hansen S, Olsen E, Raundal M, Agerholm JS.Cerebellar abiotrophy (CA) is an uncommon hereditary neurodegenerative disorder affecting the cerebellar Purkinje cells. Equine CA has been reported in several breeds, but a genetic etiology has only been confirmed in the Arabian breed, where CA is caused by an autosomal recessive mutation. Methods: Clinical and histological findings consistent with CA are reported in an 8.5-month-old Icelandic filly. The filly showed a perceived sudden onset of marked head tremor, incoordination, ataxia, lack of menace response and a broad-based stance. Cerebrospinal fluid, hematological and biochemical findi...
Szmatoła T, Gurgul A, Jasielczuk I, Oclon E, Ropka-Molik K, Stefaniuk-Szmukier M, Polak G, Tomczyk-Wrona I, Bugno-Poniewierska M.The present study reports runs of homozygosity (ROH) distribution in the genomes of six horse breeds (571 horses in total) representing three horse types (primitive, light, and draft horses) based on the 65k Equine BeadChip assay. Of major interest was the length, quantity, and frequency of ROH characteristics, as well as differences between horse breeds and types. Noticeable differences in the number, length and distribution of ROH between breeds were observed, as well as in genomic inbreeding coefficients. We also identified regions of the genome characterized by high ROH coverage, known as ...
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....
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...
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...
Colpitts J, McLoughlin PD, Poissant J.Understanding inbreeding and its impact on fitness and evolutionary potential is fundamental to species conservation and agriculture. Long stretches of homozygous genotypes, known as runs of homozygosity (ROH), result from inbreeding and their number and length can provide useful population-level information on inbreeding characteristics and locations of signatures of selection. However, the utility of ROH for conservation is limited for natural populations where baseline data and genomic tools are lacking. Comparing ROH metrics in recently feral vs. domestic populations of well understood spe...
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...
Cai D, Zhu S, Gong M, Zhang N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang X, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D....The exceptionally rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses, and zebras represent three extant subgenera of lineage, while the subgenus is another remarkable lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from Northern China in the Holocene that could be assigned morphologically and genetically to , a species representative of . We present the first high-quality complete genome of the lineage, which was sequenced to 13.4× depth of coverage. Radioc...
Orlando L, Librado P.Domestication has changed the natural evolutionary trajectory of horses by favoring the reproduction of a limited number of animals showing traits of interest. Reduced breeding stocks hampered the elimination of deleterious variants by means of negative selection, ultimately inflating mutational loads. However, ancient genomics revealed that mutational loads remained steady during most of the domestication history until a sudden burst took place some 250 years ago. To identify the factors underlying this trajectory, we gather an extensive dataset consisting of 175 modern and 153 ancient genome...
Hamann H, Distl O.A data set constituting a total of 310,109 Hanoverian warmblood horses was analyzed to ascertain the genetic variability, coefficients of inbreeding, and gene contributions of foreign populations. The reference population contained all Hanoverian horses born from 1980 to 2000. In addition, Hanoverian stallions born from 1980 to 1995 and Hanoverian breeding mares from the birth years 1980 to 1995 with registered foals were analyzed for the same genetic parameters. The average complete generation equivalent was approximately 8.43 for the reference population. The mean coefficient of inbreeding w...
The Journal of heredityDecember 28, 2018
Volume 110, Issue 2 173-182 doi: 10.1093/jhered/esy061
Sadeghi R, Moradi-Shahrbabak M, Miraei Ashtiani SR, Schlamp F, Cosgrove EJ, Antczak DF.The principal aims of this study were to explore genetic diversity and genome-wide selection signatures in Persian Arabian horses and to determine genetic relationship of Persian Arabians with other Iranian horse breeds. We evaluated 71 horses from 8 matrilineal strains tracing to 47 mares from the mid to late 19th century, using the equine 670k single nucleotide polymorphism (SNP) BeadChip. Mean observed and expected heterozygosity were (0.43) and (0.45), respectively, average inbreeding measures (inbreeding estimates based on runs of homozygosity and pedigree information) were low, indicatin...
Giontella A, Sarti FM, Cardinali I, Giovannini S, Cherchi R, Lancioni H, Silvestrelli M, Pieramati C.The Sardinian Anglo Arab (SAA) is a famous horse breed in Italy, with a significant historical background in the island of Sardinia. The aim of the study is to perform an evaluation of genetic variability in SAA using pedigree and mitochondrial data. In the current population, pedigree completeness was observed to be close to 100%, while the inbreeding coefficient and the average relatedness were lower than 3%. The ratio of effective founders/numbers of ancestors was 3.68 for the whole pedigree. The effective population size (N) computed by an individual increase in inbreeding (N) was 456.86, ...
Langlois B, Blouin C.Declarations of matings (535,746) and 308,549 consecutive declarations of birth from 1989 to 1999 were analysed by logistic regression in order to determine the effects of year, breed and age of parents on numerical productivity (the number of foals declared per mated mare per year). For the years 1994 to 1999, the status of the mare, type of mating and month of first mating, were also available. The effect of inbreeding and, for warm-blooded horses, the effect of the level of performances or the effect of the level of breeding value estimation were also analysed. The main results are the foll...
Leegwater PA, Vos-Loohuis M, Ducro BJ, Boegheim IJ, van Steenbeek FG, Nijman IJ, Monroe GR, Bastiaansen JW, Dibbits BW, van de Goor LH, Hellinga I....Inbreeding and population bottlenecks in the ancestry of Friesian horses has led to health issues such as dwarfism. The limbs of dwarfs are short and the ribs are protruding inwards at the costochondral junction, while the head and back appear normal. A striking feature of the condition is the flexor tendon laxity that leads to hyperextension of the fetlock joints. The growth plates of dwarfs display disorganized and thickened chondrocyte columns. The aim of this study was to identify the gene defect that causes the recessively inherited trait in Friesian horses to understand the disease proce...
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...
Physick-Sheard P, Kraus M, Basrur P, McGurrin K, Kenney D, Schenkel F.To assess evidence for genetic contributions to atrial fibrillation (AF) in the Standardbred horse. Methods: Equine referrals to the Ontario Veterinary College Health Sciences Centre (OVCHSC) for 1985-2009, and age and gait matched breed registry controls. Methods: Breeds presenting ≥ 5 times annually were tabulated (admission year and diagnosis; total 40,039; AF 396; no AF 39,643), and breed and year effects examined. Heritability and inbreeding coefficients were determined for Standardbred AF cases and racing contemporaries, and odds ratios for AF were calculated for frequently occurring s...
Fawcett JA, Sato F, Sakamoto T, Iwasaki WM, Tozaki T, Innan H.The domestication process of plants and animals typically involves intense inbreeding and directional selection for various traits. Here, we genotyped 370 Japanese Thoroughbred horses using the recently developed 670k SNP array and performed various genome-wide analysis also using genotype data of other horse breeds. We identified a number of regions showing interesting patterns of polymorphisms. For instance, the region containing the MC1R locus associated with chestnut coat color may have been targeted by selection for a different mutation much earlier on than the recent selection for chestn...
Curik I, Zechner P, Sölkner J, Achmann R, Bodo I, Dovc P, Kavar T, Marti E, Brem G.While the negative effects of inbreeding and reduced heterozygosity on fecundity and survival are well established, only a few investigations have been carried out concerning their influence on morphological traits. This topic is of particular interest for a small and closed population such as the Lipizzan horse. Thus, 27 morphological traits were measured in 360 Lipizzan mares and were regressed on the individual inbreeding coefficients, as well as on the individual heterozygosity and mean squared distances (mean d(2)) between microsatellite alleles within an individual. Both individual heter...
Holmes CM, Violette N, Miller D, Wagner B, Svansson V, Antczak DF.The Icelandic horse has been maintained as a closed population in its eponymous homeland for many generations, with no recorded introductions of new horses of any breed since the year 1000 CE. Here we determined the diversity of major histocompatibility complex (MHC) haplotypes in 156 Icelandic horses from two groups, based on a panel of 12 polymorphic intra-MHC microsatellites tested in families of various composition. We identified a total of 79 MHC haplotypes in these two groups, including one documented intra-MHC recombination event from a total of 147 observed meioses. None of these MHC h...
Sandmeyer LS, Kingsley NB, Walder C, Archer S, Leis ML, Bellone RR, Bauer BS.To characterize clinical manifestations, measure frequency, and evaluate risk factors for equine recurrent uveitis (ERU) in Appaloosa horses in western Canada. Methods: 145 Appaloosa horses. Methods: Ophthalmic examinations were completed and eyes were classified as having no or mild clinical signs, or moderate, or severe damage from ERU. Clinical signs, age, sex, base coat color, and pattern were recorded. Whole blood and/or mane hair follicles were collected for DNA extraction, and all horses were tested for the leopard complex (LP) spotting pattern allele. Pedigree analysis was completed on...
Bussiman FO, Perez BC, Ventura RV, Peixoto MGCD, Curi RA, Balieiro JCC.Genetic improvement, without control of inbreeding, can go to loss of genetic variability, reducing the potential for genetic gains in the domestic populations. The aim of this study was to analyze the population structure and the inbreeding depression in Campolina horses. Phenotype information from 43 465 individuals was analyzed, data provided by the Campolina Breeders Association. A pedigree file containing 107 951 horses was used to connected the phenotyped individuals. The inbreeding coefficient was performed by use of the diagonal of the relationship matrix and the genealogical parameter...
The Journal of hereditySeptember 13, 2007
Volume 98, Issue 6 594-602 doi: 10.1093/jhered/esm064
Plante Y, Vega-Pla JL, Lucas Z, Colling D, de March B, Buchanan F.The present-day Sable Island horse population, inhabiting an island off the eastern coast of Canada, is believed to have originated mainly from horses confiscated from the early French settlers in Nova Scotia in the latter half of the 18th century. In 1960, the Sable Island horses were given legal protected status and no human interference has since been allowed. The objective of this study was to characterize the current genetic diversity in Sable Island horses in comparison to 15 other horse breeds commonly found in Canada and 5 Spanish breeds. A total of 145 alleles from 12 microsatellite l...
Sairanen J, Nivola K, Katila T, Virtala AM, Ojala M.The Finnish mating records of Standardbred trotters (SB; n = 33 679) and Finnhorses (FH; n = 32 731) were analysed to study the effect of the level of inbreeding on foaling rates and to estimate the heritability of foaling rate. A linear mixed model was assumed, with the outcome of the foaling (foal or no foal) as the trait of the study. A restricted maximum likelihood-based method was used to calculate the estimates of the variance components. Predictions of breeding values and estimates of fixed effects were also calculated. The average level of inbreeding was 9.9% in the SB and 3.6% in the ...
The Journal of heredityMay 1, 1984
Volume 75, Issue 3 220-224 doi: 10.1093/oxfordjournals.jhered.a109916
Cothran EG, MacCluer JW, Weitkamp LR, Pfennig DW, Boyce AJ.The relationship between inbreeding and both conception and foaling rates in Standardbred horses (trotters and pacers) was examined for 1194 breeding years. There was a statistically significant (P less than 0.05) trend for conception and foaling rates to decrease with increased inbreeding; however, this relationship accounted for less than 2 percent of the variation. Additionally, the relationship between reproductive performance and inbreeding was not consistent between trotters and pacers. For trotters (F = 0.103) there was a trend for an increase in conception and foaling rates with increa...
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 ...
van Eldik P, van der Waaij EH, Ducro B, Kooper AW, Stout TA, Colenbrander B.Inbreeding is widely believed to negatively affect reproductive performance. Indeed, in some species, high levels of inbreeding are thought to be the major cause of poor semen quality. It is, however, not clear whether inbreeding affects fertility in horses. In this study, the relationship between inbreeding and semen quality was examined in 285 immature Shetland pony stallions submitted for breeding soundness examination in March-April of the years 1992-1997. The majority of stallions examined were 3 years old (85%) and their coefficients of inbreeding ranged from 0 to 25% (mean+/-S.D.: 3+/-4...
Criscione A, Mastrangelo S, D'Alessandro E, Tumino S, Di Gerlando R, Zumbo A, Marletta D, Bordonaro S.Purosangue Orientale Siciliano, Sanfratellano and Siciliano represent the Sicilian equine genetic resource. This study aimed to investigate the genetic diversity, population structure and the pattern of autozygosity of Sicilian horse populations using genome-wide single-nucleotide polymorphism (SNP) data generated with the Illumina Equine SNP70 array. The genotyping data of 17 European and Middle East populations were also included in the study. The patterns of genetic differentiation, model-based clustering and Neighbour-Net showed the expected positioning of Sicilian populations within the w...
Szmatoła T, Gurgul A, Jasielczuk I, Oclon E, Ropka-Molik K, Stefaniuk-Szmukier M, Polak G, Tomczyk-Wrona I, Bugno-Poniewierska M.The present study reports runs of homozygosity (ROH) distribution in the genomes of six horse breeds (571 horses in total) representing three horse types (primitive, light, and draft horses) based on the 65k Equine BeadChip assay. Of major interest was the length, quantity, and frequency of ROH characteristics, as well as differences between horse breeds and types. Noticeable differences in the number, length and distribution of ROH between breeds were observed, as well as in genomic inbreeding coefficients. We also identified regions of the genome characterized by high ROH coverage, known as ...
Sánchez-Guerrero MJ, Solé M, Azor PJ, Sölkner J, Valera M.Vitiligo and melanoma are relatively common disorders in grey Pura Raza Español horses and other horse breeds with grey-coloured coats. Objective: To determine the breed prevalence, environmental risks factors and estimate the genetic parameters for vitiligo and melanoma in Pura Raza Español horses. Methods: Retrospective cohort study. Methods: We analysed data from a large worldwide population of Pura Raza Español horses. The database included the vitiligo and melanoma scores, on either a four- or six-point linear scale, of 11,436 horses. Genetic parameters were estimated using a Bayesian ...
Giontella A, Sarti FM, Biggio GP, Giovannini S, Cherchi R, Pieramati C, Silvestrelli M.The purpose of this study was to estimate the heritability and genetic correlations of four biometric measurements and an overall score (OS) in the Sardinian Anglo-Arab horse (SAA); moreover, the effect of inbreeding on these traits was investigated. A dataset with 43,624 horses (27,052 females and 16,572 males) was provided by the Agricultural Research Agency of Sardinia (AGRIS). Cannon bone circumference (BC), chest girth (CG), shoulder length (SL), and withers height (WH) were measured on 6033 SAA horses born in Sardinia between 1967 and 2005; beside the measurements, an overall score (OS) ...
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 ...
Ducro BJ, Schurink A, Bastiaansen JW, Boegheim IJ, van Steenbeek FG, Vos-Loohuis M, Nijman IJ, Monroe GR, Hellinga I, Dibbits BW, Back W, Leegwater PA.Hydrocephalus in Friesian horses is a developmental disorder that often results in stillbirth of affected foals and dystocia in dams. The occurrence is probably related to a founder effect and inbreeding in the population. The aim of our study was to find genomic associations, to investigate the mode of inheritance, to allow a DNA test for hydrocephalus in Friesian horses to be developed. In case of a monogenic inheritance we aimed to identify the causal mutation. Results: A genome-wide association study of hydrocephalus in 13 cases and 69 controls using 29,720 SNPs indicated the involvement o...
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...
Todd ET, Fromentier A, Sutcliffe R, Running Horse Collin Y, Perdereau A, Aury JM, Èche C, Bouchez O, Donnadieu C, Wincker P, Kalbfleisch T....Historical genomes can provide important insights into recent genomic changes in horses, especially the development of modern breeds. In this study, we characterized 8.7 million genomic variants from a panel of 430 horses from 73 breeds, including newly sequenced genomes from 20 Clydesdales and 10 Shire horses. We used this modern genomic variation to impute the genomes of four historically important horses, consisting of publicly available genomes from 2 Przewalski's horses, 1 Thoroughbred, and a newly sequenced Clydesdale. Using these historical genomes, we identified modern horses with high...
Chen C, Zhu B, Tang X, Chen B, Liu M, Gao N, Li S, Gu J.In the genomes of diploid organisms, runs of homozygosity (ROH), consecutive segments of homozygosity, are extended. ROH can be applied to evaluate the inbreeding situation of individuals without pedigree data and to detect selective signatures via ROH islands. We sequenced and analyzed data derived from the whole-genome sequencing of 97 horses, investigated the distribution of genome-wide ROH patterns, and calculated ROH-based inbreeding coefficients for 16 representative horse varieties from around the world. Our findings indicated that both ancient and recent inbreeding occurrences had vary...
Kim NY, Seong HS, Kim DC, Park NG, Yang BC, Son JK, Shin SM, Woo JH, Shin MC, Yoo JH, Choi JW.The Jeju horse is an indigenous Korean horse breed that is currently registered with the Food and Agriculture Organization of the United Nations. However, there is severe lack of genomic studies on Jeju horse. This study was conducted to investigate genetic characteristics of horses including Jeju horse, Thoroughbred and Jeju crossbred (Jeju × Thoroughbred) populations. We compared the genomes of three horse populations using the Equine SNP70 Beadchip array. Short-range Linkage disequilibrium was the highest in Thoroughbred, whereas r values were lowest in Jeju horse. Expected heterozygos...
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...
