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Topic:Inbreeding
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.
Pedigree Analysis of Warmblood Horses Participating in Competitions for Young Horses. The aim of the study was to characterize the population structure and assess the genetic diversity of warmblood horses used in the show jumping discipline. Pedigree data of 1,048 horses participating in the Polish Championships for Young Horses were analyzed. The pedigree of these animals included 12 863 individuals. The study consisted in analysis of the pedigree structure of the horses and characterization of the homozygosity and genetic diversity in the population. It was found that pedigree completeness and depth were sufficient for reliable assessment of the genetic diversity in the analy...
Genetic Variability and Population Structure of Polish Konik Horse Maternal Lines Based on Microsatellite Markers. The aim of the conservation programme is to maintain the population size of endangered livestock breeds of less economic importance at a level that ensures the survival of the breed, the preservation of genetic diversity, and the preservation of as many pedigree lines as possible. The Polish Konik, a native Polish primitive-type horse breed and is one of the breeds included in such a programme in Poland. Presently, there are only 16 (of the 35 maternal lines known in 1962), some of which are endangered. We examined the genetic variability and structure of the Polish Konik maternal lines (176 i...
Suitability of Pedigree Information and Genomic Methods for Analyzing Inbreeding of Polish Cold-Blooded Horses Covered by Conservation Programs. Traditionally, pedigree-based relationship coefficients were used to manage inbreeding and control inbreeding depression that occurs within populations. The extensive incorporation of genomic data in livestock breeding creates the opportunity to develop and implement methods to manage populations at the genomic level. Consequently, the realized proportion of the genome that two individuals share can be more accurately estimated instead of using pedigree information to estimate the expected proportion of shared alleles. To make use of this improvement, in this study we evaluated the genomic inb...
Investigating the population structure and genetic diversity of Arabian horses in Oman using SNP markers. Arabian horses were selected for metabolic efficiency, beauty, efficiency and endurance. Therefore, Bedouins have for centuries traced their prized horses' ancestries. With the establishment of the World Arabian Horse Organization (WAHO), registration of Arabian horses became centralized and countries worldwide registered them in its database. Most existing Arabian horses in Oman today were imported after the 1970s and are predominantly flat-racing Arabians. This work aimed at revealing the genetic background and diversity of Omani Arabian horses by comparing them with Arabian horses from a di...
Genomic comparisons of Persian Kurdish, Persian Arabian and American Thoroughbred horse populations. The present research aimed to characterize the Persian Kurdish horse population relative to the Persian Arabian and American Thoroughbred populations using genome-wide SNP data. Fifty-eight Kurdish, 38 Persian Arabian and 83 Thoroughbred horses were genotyped across 670,796 markers. After quality control and pruning to eliminate linkage disequilibrium between loci which resulted in 13,554 SNPs in 52 Kurdish, 24 Persian Arabian and 58 Thoroughbred horses, the Kurdish horses were generally distinguished from the Persian Arabian samples by Principal Component Analyses, cluster analyses and calcul...
Impaired Reproductive Function in Equines: From Genetics to Genomics. Fertility is one of the key factors in the economic and productive success of the equine industry. Despite this, studies on the genetic causes affecting reproductive performance are scarce, especially in mares, where the genetic architecture of the reproductive traits is extremely complex. Today, with the increasing availability of new genomic methodologies for this species, we are presented with an interesting opportunity to understand the genetic basis of equine reproductive disorders. These include, among others, novel techniques for detecting chromosomal abnormalities, whose association wi...
Discriminant Canonical Analysis of the Contribution of Spanish and Arabian Purebred Horses to the Genetic Diversity and Population Structure of Hispano-Arabian Horses. Genetic diversity and population structure were analyzed using the historical and current pedigree information of the Arabian (PRá), Spanish Purebred (PRE), and Hispano-Arabian (Há) horse breeds. Genetic diversity parameters were computed and a canonical discriminant analysis was used to determine the contributions of ancestor breeds to the genetic diversity of the Há horse. Pedigree records were available for 207,100 animals born between 1884 and 2019. Nei's distances and the equivalent subpopulations number indicated the existence of a highly structured, integrated population for the Há ...
Analysis of the Pedigree and Ancestors of the Cutting Population of the Quarter Horse Breed. 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...
Analysis of Genetic Variability in the Argentine Polo Horse With a Panel of Microsatellite Markers. Argentine Polo (AP) is a young horse breed with a fast expansion because of an open registry policy and the application of assisted reproduction technologies. In the last years, AP showed a remarkable progress associated with the use of embryo transfer technology and intensive selection based on sport performance. However, these practices could have affected the genetic variability of the breed. To monitor these potential changes, a parentage panel of 11-15 microsatellites was investigated for changes in allele frequencies, heterozygosity, and exclusion probability over a 16 year period. Frequ...
Genetic analysis of the endangered Cleveland Bay horse: A century of breeding characterised by pedigree and microsatellite data. The Cleveland Bay horse is one of the oldest equines in the United Kingdom, with pedigree data going back almost 300 years. The studbook is essentially closed and because of this, there are concerns about loss of genetic variation across generations. The breed is one of five equine breeds listed as "critical" (<300 registered adult breeding females) by the UK Rare Breeds Survival Trust in their annual Watchlist. Due to their critically endangered status, the current breadth of their genetic diversity is of concern, and assessment of this can lead to improved breed management strategies. Her...
Genetic inbreeding depression load for morphological traits and defects in the Pura Raza Española horse. 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 ...
Fine-scale estimation of inbreeding rates, runs of homozygosity and genome-wide heterozygosity levels in the Mangalarga Marchador horse breed. With the availability of high-density SNP panels and the establishment of approaches for characterizing homozygosity and heterozygosity sites, it is possible to access fine-scale information regarding genomes, providing more than just comparisons of different inbreeding coefficients. This is the first study that seeks to access such information for the Mangalarga Marchador (MM) horse breed on a genomic scale. To this end, we aimed to assess inbreeding levels using different coefficients, as well as to characterize homozygous and heterozygous runs in the population. Using Axiom ® Equine Genoty...
Is similarity in Major Histocompatibility Complex (MHC) associated with the incidence of retained fetal membranes in draft mares? A cross-sectional study. The failure of the maternal immune system to recognize fetal antigens and vice versa due to MHC similarity between the foal and its dam might result in the lack of placental separation during parturition in mares. The aim of the study was to investigate the influence of MHC similarity between a mare and a foal on the incidence of retained fetal membranes (RFM) in post-partum mares. DNA was sampled from 43 draft mares and their foals. Mares which failed to expel fetal membranes within three hours after foal expulsion were considered the RFM group (n = 14) and mares that expelled fetal membranes...
Genetic Structure Analysis of the Pura Raza Español Horse Population through Partial Inbreeding Coefficient Estimation. The aim of this work was to analyze genetic parameters such as the inbreeding coefficient (F), relatedness coefficient (AR) and partial inbreeding coefficient (Fij) of the whole PRE population, and the ancestors which account for 50% of the total genetic variability of the current population, from genealogical information. The average F of the whole PRE population (328,706 animals) has decreased from 8.45% to 7.51% in the least 20 years. The Fij was estimated for the whole PRE population, resulting in a database of 58,772,533 records containing one record for each Fij that each animal receives...
A genome-wide scan for candidate lethal variants in Thoroughbred horses. Domestic animal populations are often characterised by high rates of inbreeding and low effective population sizes due to selective breeding practices. These practices can result in otherwise rare recessive deleterious alleles drifting to high frequencies, resulting in reduced fertility rates. This study aimed to identify potential recessive lethal haplotypes in the Thoroughbred horse breed, a closed population that has been selectively bred for racing performance. In this study, we identified a haplotype in the LY49B gene that shows strong evidence of being homozygous lethal, despite having h...
Genetic Diversity and Population Structure of Arabian Horse Populations Using Microsatellite Markers. Understanding the genetic diversity and the relationships among the show Arabian horse populations is a current issue for breeders and professionals. This study aimed to define the relationship among the Desert breed, the Straight Egyptian, and the Polish Arabian populations by considering the historical background of their origin and to verify their genetic diversity. All selected samples were related to Arabian show activities. One hundred forty four hair samples were collected from horses at stud farms having notoriety in the breeding of Arabians from different geographic regions. A set of ...
Historical Changes and Description of the Current Hungarian Hucul Horse Population. Gene conservation and management of small populations requires proper knowledge of the background and history of the breed. The aim of the study was the evaluation of population structure and changes of the Hungarian Hucul horse population. Population changes were described for the actual breeding stock as well as for groups of 10-year epochs reflecting major periods of change in the breed. Pedigree data of the registered population were analyzed using Endog and GRain software. The average value of equivalent complete generations was above nine for the actual breeding population. The longest g...
A retrospective study on semen quality parameters from four different Dutch horse breeds with different levels of inbreeding. A high degree of inbreeding has been reported to negatively impact semen quality in Friesian horses and Shetland ponies. Both breeds are characterized by a closed studbook, small population size, and high incidence of inbreeding. The Dutch Warmblood studbook (KWPN: Koninklijk Warmblood Paardenstamboek Nederland) is a much larger studbook with two distinct populations: the KWPN-Riding horses, managed as an 'open' studbook, and the KWPN-Harness horses, representing a much smaller subpopulation within the KWPN breed and managed as an 'almost closed' studbook. It was recently reported that the deg...
Dynamics of the Inbreeding Coefficient and Homozygosity in Thoroughbred Horses in Russia. The Thoroughbred (TB) horse has hugely impacted the development of horse breeding around the world. This breed has unique genetic qualities due to having had a closed studbook for approximately 300 years. In Russia, TBs have been bred since the second half of the 18th century. Here, we analyzed the genetic diversity and the inbreeding level in TB horses (n = 9680) for the period from 1990 to 2018 using polymorphisms of 17 microsatellite loci. We found that the genetic structure of the TB breed in Russia is represented by 100 alleles of panel STR (short tandem repeat) loci and has been stable f...
Genetic Variability and Population Structure in the Sardinian Anglo-Arab Horse. 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, ...
Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data. Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed ba...
Genetic Parameters and Inbreeding Effect of Morphological Traits in Sardinian Anglo Arab Horse. 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) ...
The effects of inbreeding on covering success, gestation length and foal sex ratio in Australian thoroughbred horses. Horses produce only one foal from an eleven-month gestation period, making the maintenance of high reproductive rates essential. Genetic bottlenecks and inbreeding can increase the frequency of deleterious variants, resulting in reduced reproductive levels in a population. In this study we examined the influence of inbreeding levels on foaling rate, gestation length and secondary sex ratio in Australian Thoroughbred mares. We also investigated the genetic change in these traits throughout the history of the breed. Phenotypic data were obtained from 27,262 breeding records of Thoroughbred mares...
Decreased genetic diversity in Kiso horses revealed through annual microsatellite genotyping. The Kiso horse is native to Japan and is on the verge of extinction. Here, we used microsatellites to characterize changes in their genetic diversity over time. We divided a population of Kiso horses that genotyped during 2007-2017 into three groups based on birth year: Group 1, 1980-1998 (70 horses); Group 2, 1999-2007 (61 horses); and Group 3, 2008-2017 (42 horses). We genotyped 31 microsatellites to calculate average number of alleles, observed heterozygosity, and expected heterozygosity. All indicators decreased across age groups. The results indicate that Kiso horses have been experiencin...
Risk factors for equine recurrent uveitis in a population of Appaloosa horses in western Canada. 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...
Genetic diversity within and between British and Irish breeds: The maternal and paternal history of native ponies. The UK and Ireland have many native pony breeds with historical and cultural importance as well as being a source of uncharacterized genetic diversity. However, there is a lack of comprehensive research investigating their genetic diversity and phylogenetic interrelationships. Many studies contain a limited number of pony breeds or small sample sizes for these breeds. This may result in erroneous grouping of pony breeds that otherwise have intricate interrelationships with each other and are not evaluated correctly when placed as a token subset of a larger dataset. This is the first study that...
Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population. The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the w...
Changes of sires in a breeding farm enables maintenance of DNA-level genetic variation in a produced herd of Hokkaido Native Horses. We investigated whether regular changes of the sire in a breeding farm of Hokkaido Native Horses (HKDs) enables the DNA-level genetic variation of the produced animals to be maintained. The genotypes of 31 microsatellite markers were identified and analyzed in 207 animals produced in a breeding farm in which the sire was replaced every 3 to 5 years. The mean allele number indicating the degree of genetic variation was 5.97 and was similar to those reported previously. The mean observed heterozygosity was 0.74 and was higher than the expected heterozygosity, 0.69; F was -0.07, indicating that ...
Genetic and Environmental Factors Influencing Gestation Length in Lusitano Horses. Breeding and parturition records collected over a period of 35 years in the Alter Real stud of Lusitano horses were used to calculate gestation length (GL). The 1027 gestations by 209 mares mated to 60 stallions had a mean GL of 338.1 ± 9.26 days. The mixed model analysis of variance indicated that the sex of the foal and inbreeding of the dam and foal had no significant effect on GL (P > .05). On the other hand, GL increased linearly with mare age, with an estimated regression coefficient of 0.155 ± 0.069 days/year (P < .05). Year and conception month affected GL (P < .05), with...
Effect of inbreeding on the “Club Foot” disorder in Arabian Pureblood horses reared in Italy. "The Club Foot" (or "Mismatched Foot") is an acquired or congenital flexural deformity of the distal interphalangeal joint, caused by a shortening of the musculotendinous unit of the deep digital flexor tendon. The aim of this research was to detect the incidence of the disorder in Arabian Pureblood horses, attempting to understand its causes and to analyze a possible role of inbreeding in its expression. In this breed, in fact, the pathology is widespread because in the environment of origin, the rocky desert, a hard and almost goat's hoof is not disabling so the selection against this disord...
