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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.
Origin and Evolution of Deleterious Mutations in Horses. 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...
Genome-wide SNP analysis of Japanese Thoroughbred racehorses. 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...
Genetic variability and history of a native Finnish horse breed. The Finnhorse was established as a breed more than 110 years ago by combining local Finnish landraces. Since its foundation, the breed has experienced both strong directional selection, especially for size and colour, and severe population bottlenecks that are connected with its initial foundation and subsequent changes in agricultural and forestry practices. Here, we used sequences of the mitochondrial control region and genomic single nucleotide polymorphisms (SNPs) to estimate the genetic diversity and differentiation of the four Finnhorse breeding sections: trotters, pony-sized horses, dr...
Genome-Wide Homozygosity Patterns and Evidence for Selection in a Set of European and Near Eastern Horse Breeds. Intensive artificial and natural selection have shaped substantial variation among European horse breeds. Whereas most equine selection signature studies employ divergent genetic population structures in order to derive specific inter-breed targets of selection, we screened a total of 1476 horses originating from 12 breeds for the loss of genetic diversity by runs of homozygosity (ROH) utilizing a 670,000 single nucleotide polymorphism (SNP) genotyping array. Overlapping homozygous regions (ROH islands) indicating signatures of selection were identified by breed and similarities/dissimilaritie...
The Genomic Makeup of Nine Horse Populations Sampled in the Netherlands. The spectrum of modern horse populations encompasses populations with a long history of development in isolation and relatively recently formed types. To increase our understanding of the evolutionary history and provide information on how to optimally conserve or improve these populations with varying development and background for the future, we analyzed genotype data of 184 horses from 9 Dutch or common horse populations in the Netherlands: The Belgian draft horse, Friesian horse, Shetland pony, Icelandic horse, Gelder horse, Groninger horse, harness horse, KWPN sport horse and the Lipizzan...
Genomic measures of inbreeding in the Norwegian-Swedish Coldblooded Trotter and their associations with known QTL for reproduction and health traits. Since the 1950s, the Norwegian-Swedish Coldblooded trotter (NSCT) has been intensively selected for harness racing performance. As a result, the racing performance of the NSCT has improved remarkably; however, this improved racing performance has also been accompanied by a gradual increase in inbreeding level. Inbreeding in NSCT has historically been monitored by using traditional methods that are based on pedigree analysis, but with recent advancements in genomics, the NSCT industry has shown interest in adopting molecular approaches for the selection and maintenance of this breed. Consequent...
MHC haplotype diversity in Icelandic horses determined by polymorphic microsatellites. 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...
Genetic screening for cerebellar abiotrophy, severe combined immunodeficiency and lavender foal syndrome in Arabian horses in Poland. The highly selective breeding of Arabian horses results in inbreeding depression and genetic disorders, thereby causing significant economic loss. The Polish population of Arabians has a great impact on many breeding programmes. The aim of the current study was to monitor genetic variants involved in the most common genetic disorders of this breed. A total of 808 elite Arabian horses were screened for cerebellar abiotrophy (CA), severe combined immunodeficiency (SCID) and lavender foal syndrome (LFS) genetic disorders by Sanger sequencing and allelic discrimination methods. The investigated po...
High-resolution population structure and runs of homozygosity reveal the genetic architecture of complex traits in the Lipizzan horse. The sample ascertainment bias due to complex population structures remains a major challenge in genome-wide investigations of complex traits. In this study we derived the high-resolution population structure and levels of autozygosity of 377 Lipizzan horses originating from five different European stud farms utilizing the SNP genotype information of the high density 700 k Affymetrix Axiom™ Equine genotyping array. Scanning the genome for overlapping runs of homozygosity (ROH) shared by more than 50% of horses, we identified homozygous regions (ROH islands) in order to investigate the gene ...
Genetic and environmental risk factors for vitiligo and melanoma in Pura Raza Español horses. 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 ...
Genetic Diversity of Persian Arabian Horses and Their Relationship to Other Native Iranian Horse Breeds. 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...
Genetic analyses for conservation of the traditional Tokara horse using 31 microsatellite markers. In order to promote conservation of the traditional Tokara horse in its remaining three breeding areas in Japan (Nakanoshima, Kaimondake, and Iriki), we genotyped 123 horses using 31 microsatellite markers and determined their genetic diversity. On average, the number of alleles (N), observed heterozygosity (H), expected heterozygosity (H), and inbreeding coefficient (F) among all horses were 3.0, 0.424, 0.481, and 0.108, respectively. Compared with other endangered horse breeds, we found that, even though the size of the Tokara horse population has recently increased, the N, H, and H of Tokar...
Evaluation of recent changes in genetic variability in Japanese thoroughbred population based on a short tandem repeat parentage panel. The integrity of thoroughbreds is maintained under strict regulation involving DNA parentage testing, which is robust in a population with high genetic variability. The genetic variability of the thoroughbred population is possibly fluctuating because of selective breeding that has focused on adaptations for racing performance. To monitor genetic variability within the population and the effectiveness of short tandem repeat (STR) parentage testing, we investigated allele frequencies and the exclusion probability (PE) of 16-17 loci of a parentage panel in the Japanese thoroughbred population ov...
Genetic variability of Akhal-Teke horses bred in Italy. The Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences. Methods: Seventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on oth...
Exploring genetic diversity in an Italian horse native breed to develop strategies for preservation and management. Genetic diversity is a key factor for both adaptation and response to selection. The loss of genetic diversity causes a decrease in individual fitness, and it has a dramatically negative effect on population lifespan in the long term. This study aimed at exploring the genetic diversity at pedigree level of the Bardigiano horse breed, which is a native breed from Italy shaped for living in rural areas. In 1977, the Bardigiano studbook was founded to preserve the breed and for improving its use for riding and draft purposes. Pedigree data contained 9,469 horses, of which 3,416 were alive. Demog...
Genome-wide analyses of the Jeju, Thoroughbred, and Jeju crossbred horse populations using the high density SNP array. 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...
Genetic structure and connectivity analysis in a large domestic livestock meta-population: The case of the Pura Raza Español horses. The Pura Raza Español (PRE) is an autochthonous Spanish horse population distributed in 65 countries and managed by a single association. Since 1960s, breeding animals have been steadily exported to other countries to establish local subpopulations. We analysed the genetic structure of a PRE horse meta-population (MP) of 215,500 animals from countries with at least 80 active animals (27 countries comprising 77% of the total animals in the complete pedigree). Genotypes from active animals (59% of the total animals in the complete pedigree) were also studied. Genetic analysis of the MP was perf...
Genetic diversity and population structure of three traditional horse breeds of Bhutan based on 29 DNA microsatellite markers. The genetic variability and population structure of three Bhutanese traditional horse breeds were assessed through genotyping of 74 horses (Boeta 25, Sharta 14 and Yuta 35) for 29 microsatellite DNA loci. Altogether, 282 alleles were detected across 29 polymorphic loci. The allelic diversity (NE) (Boeta 4.94; Sharta 4.65; Yuta 5.30) and gene diversities (HE) (Boeta 0.78; Sharta 0.77; Yuta 0.79) were high. None of the breeds deviated significantly from the Hardy-Weinberg equilibrium. There was no sign of significant population bottleneck for all the breeds. The inbreeding estimates (FIS) of the...
Analysis of founders and performance test effects on an autochthonous horse population through pedigree analysis: structure, genetic variability and inbreeding. The Maremmano is an autochthonous Italian horse breed, which probably descended from the native horses of the Etruscans (VI century B.C.); the Studbook was acknowledged in 1980, and it includes 12 368 horses born from that year up to 2015. The aim of this study was to evaluate the effect of the selection program on the genetic variability of the Maremmano population; the analysis was performed using both the 'Endog v 4.8' program available at http://webs.ucm.es/info/prodanim/html/JP_Web.htm and in-house software on official pedigree data. Four Reference Populations were considered, and the mos...
Elevated urinary excretion of free pyridinoline in Friesian horses suggests a breed-specific increase in collagen degradation. Friesian horses are known for their high inbreeding rate resulting in several genetic diseases such as hydrocephaly and dwarfism. This last decade, several studies focused on two other presumed hereditary traits in Friesian horses: megaoesophagus and aortic rupture. The pathogenesis of these diseases remains obscure but an important role of collagen has been hypothesized. The purpose of this study was to examine possible breed-related differences in collagen catabolism. Urinary specimens from Friesian (n = 17, median age 10 years old) and Warmblood horses (n = 17, median age 10 years...
Founder-specific inbreeding depression affects racing performance in Thoroughbred horses. The Thoroughbred horse has played an important role in both sporting and economic aspects of society since the establishment of the breed in the 1700s. The extensive pedigree and phenotypic information available for the Thoroughbred horse population provides a unique opportunity to examine the effects of 300 years of selective breeding on genetic load. By analysing the relationship between inbreeding and racing performance of 135,572 individuals, we found that selective breeding has not efficiently alleviated the Australian Thoroughbred population of its genetic load. However, we found evidenc...
Pedigree analysis and inbreeding effects over morphological traits in Campolina horse population. 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...
Determinants of gestation length in Thoroughbred mares on German stud farms. The aim of the present study was to analyze the effects of stallion and mare, their ages, and maternal lineage on the gestation length (GL) in Thoroughbreds. In addition, additive genetic effects of the dam, stallion and fetus were analyzed. Data were taken from 1993 through 2009, and included 16,226 pregnancies from 5959 Th oroughbred mares mated with 290 different stallions. All analyses were performed using linear mixed models. The GL ranged from 306 to 390 days, with a mean length of 347.0 ± 14.4 days. Mating of mares with stallions aged 17 years and older resulted in a significantly ...
Genetic analysis of maternal and paternal lineages in Kabardian horses by uniparental molecular markers. Studies of mitochondrial DNA (mtDNA) as well as the non-recombining part of the Y chromosome help to understand the origin and distribution of maternal and paternal lineages. The Kabardian horse from Northern Caucasia which is well-known for strength, stamina and endurance in distance riding has a large gap in its breeding documentation especially in the recent past. A 309 bp fragment of the mitochondrial D-loop (156 Kabardian horses) and six mutations in Y chromosome (49 Kabardian stallions), respectively, were analyzed to get a better insight into breeding history, phylogenetic relationship ...
Genetic analysis of the Hungarian draft horse population using partial mitochondrial DNA D-loop sequencing. The Hungarian draft is a horse breed with a recent mixed ancestry created in the 1920s by crossing local mares with draught horses imported from France and Belgium. The interest in its conservation and characterization has increased over the last few years. The aim of this work is to contribute to the characterization of the endangered Hungarian heavy draft horse populations in order to obtain useful information to implement conservation strategies for these genetic stocks. Methods: To genetically characterize the breed and to set up the basis for a conservation program, in the present study a...
Genetic monitoring of horses in the Czech Republic: A large-scale study with a focus on the Czech autochthonous breeds. We propose the first comprehensive in-depth study monitoring horses in the Czech Republic. We scanned 9,289 animals from 44 populations for 17 equine STRs. Other equids analysed involved Equus przewalskii and Equus asinus. The total of 228 different alleles were detected, with the mean number of 13.4 per locus. The highest allelic richness (AR) was found in the Welsh Part Bred (6.01), followed by the Camargue (5.93) and Czech Sport Pony (5.91), whereas the Friesian exhibited the lowest AR (3.06). Interpopulation differences explained approximately nine per cent of the total genetic diversity. ...
Population Networks Associated with Runs of Homozygosity Reveal New Insights into the Breeding History of the Haflinger Horse. Within the scope of current genetic diversity analyses, population structure and homozygosity measures are independently analyzed and interpreted. To enhance analytical power, we combined the visualization of recently described high-resolution population networks with runs of homozygosity (ROH). In this study, we demonstrate that this approach enabled us to reveal important aspects of the breeding history of the Haflinger horse. We collected high-density genotype information of 531 horses originating from 7 populations which were involved in the formation of the Haflinger, namely 32 Italian Ha...
Assessment of genomic inbreeding in Polish Konik horses. The aim of this study was to assess the inbreeding coefficient of Polish Konik horses based on runs of homozygosity (ROH). Ninety six horses kept in 6 herds located across Poland were genotyped with the use of EquineSNP60 BeadChip (Illumina). SNP markers with a Minor Allele Frequency lower than 0.01 and SNPs assigned to chromosome X or Y were excluded from the study. A total of 50 708 SNPs were included for statistical analysis (SVS software, Golden Helix). The analysis showed that the population is in genetic equilibrium, with He and Ho estimates both equal to 0.3086. Seven categories of Runs...
Effects of inbreeding and other systematic effects on fertility of Black Forest Draught horses in Germany. The Black Forest Draught horse (BFDH) is an endangered German coldblood breed with its origin in the area of the Black Forest in South Germany. In this retrospective study, the influence of the inbreeding coefficient on foaling rates was investigated using records from ten breeding seasons. Due to the small population size of BFDH, the level of inbreeding is increasing and may have an effect on foaling rates.The data of the present study included all coverings reported for 1024 BFDH mares in the years 2001-2009. These mares were covered by 32 BFDH stallions from the State Stud Marbach. Data fr...
Investigation of genetic diversity and inbreeding in a Japanese native horse breed for suggestions on its conservation. Because native breeds can serve as genetic resources for adapting to environment changes, their conservation is important for future agroecosystems. Using pedigree analysis, we investigated genetic diversity and inbreeding in Japanese Hokkaido native horses, which have adapted to a cold climate and roughage diet. Genetic diversity was measured as the number of founders and the effective number of founders, ancestors and genomes. All metrics imply a decrease in genetic diversity. A comparison of these metrics suggested that pedigree bottlenecks contributed more than did random gene losses to th...
