Topic:Microsatellites
Microsatellites, also known as short tandem repeats (STRs), are repetitive sequences of DNA that consist of short motifs repeated in tandem. In horses, these genetic markers are distributed throughout the genome and exhibit high levels of polymorphism, making them valuable tools in genetic studies. Microsatellites are commonly used in parentage verification, genetic diversity assessments, and population structure analyses in equine research. They provide insights into hereditary traits and can assist in the management of breeding programs. This page compiles peer-reviewed research studies and scholarly articles that explore the application, variation, and genetic implications of microsatellites in horse populations.
Equine Multiple Congenital Ocular Anomalies maps to a 4.9 megabase interval on horse chromosome 6. Equine Multiple Congenital Ocular Anomalies (MCOA) syndrome consists of a diverse set of abnormalities predominantly localized to the frontal part of the eye. The disease is in agreement with a codominant mode of inheritance in our horse material. Animals presumed to be heterozygous for the mutant allele have cysts originating from the temporal ciliary body, peripheral retina and/or iris. In contrast, animals predicted to be homozygous for the disease-causing allele possess a wide range of multiple abnormalities, including iridociliary and/or peripheral retinal cysts, iridocorneal angle abnorm...
Genetic characterization and polymorphisms for parentage testing of the Jeju horse using 20 microsatellite loci. Genetic characterization of the Jeju horse (JH) was performed to construct a correct pedigree of the JH family. A total of 111 horses including 79 JH were genotyped using 20 microsatellite loci. The number of alleles varied from 5 to 11 (mean 7.45) in the JH. The observed heterozygosity and expected heterozygosity ranged from 0.293 to 0.891 and from 0.357 to 0.841, respectively. The polymorphic information contents (PIC) ranged from 0.335 to 0.816. AHT4, ASB2, ASB17, ASB23, CA425, HMS2, HMS3, HTG10, LEX3 and VHL20 loci had relatively high PIC values (> 0.7). The total exclusion probability ...
Genetic analysis, breed assignment and conservation priorities of three native Danish horse breeds. A genetic analysis was performed on three indigenous Danish horse breeds using 12 microsatellite markers from a standard kit for parental testing. These three breeds are all considered endangered based on their small population sizes. Genetic variation in these three breeds was comparable to other horse breeds in Europe, and they do not seem to be at immediate danger of extinction caused by genetic deterioration. The Knabstrupper breed had more genetic variation, as measured by expected heterozygosity and allelic richness, than the other two breeds (Frederiksborg and Jutland). F(ST) statistics...
Single nucleotide polymorphisms of interleukin-1 beta related genes and their associations with infection in the horse. In previous work, we found significant associations of horse chromosome 15 (ECA15) microsatellite markers HMSO1 and HTG06 with two horse infections, Rhodococcus equi and Lawsonia intracellularis, respectively. Interleukin-1 beta subunit and interleukin-1 receptor antagonist encoding genes (IL1B and IL1RN) could be considered as candidate genes underlying the associations reported. Therefore, we identified single nucleotide polymorphisms (SNPs) within three interleukin-1 beta functionally related genes: IL1B, IL1RN and Casp1 (interleukin-1 beta converting enzyme/caspasel encoding gene). Using a...
Missense mutation in exon 2 of SLC36A1 responsible for champagne dilution in horses. Champagne coat color in horses is controlled by a single, autosomal-dominant gene (CH). The phenotype produced by this gene is valued by many horse breeders, but can be difficult to distinguish from the effect produced by the Cream coat color dilution gene (CR). Three sires and their families segregating for CH were tested by genome scanning with microsatellite markers. The CH gene was mapped within a 6 cM region on horse chromosome 14 (LOD = 11.74 for theta = 0.00). Four candidate genes were identified within the region, namely SPARC [Secreted protein, acidic, cysteine-rich (osteonectin)], SL...
[Genetics of recurrent airway obstruction (RAO)]. Recurrent airway obstruction (RAO) is a multifactorial and polygenic disease. Affected horses are typically 7 years of age or older and show exercise intolerance, increased breathing effort, coughing, airway neutrophilia, mucus accumulation and hyperreactivity as well as cholinergic bronchospasm. The environmental factors responsible are predominantly allergens and irritants in haydust, but the immunological mechanisms underlying RAO are still unclear. Several studies have demonstrated a familiar predisposition for RAO and it is now proven that the disease has a genetic basis. In offspring, th...
Genetic analysis of the Hispano-Breton heavy horse. Hispano-Breton (HB) is a horse breed with a recent mixed ancestry. It was developed in the 1930s by crossing local mares with Breton draught horses imported from France. Nowadays it is considered to be in a vulnerable situation due to census decline. To genetically characterize the breed and to set up the basis for a conservation programme, we have employed two types of molecular markers: a 347-bp D-loop mitochondrial DNA (mtDNA) fragment and 13 microsatellite loci. A representative sample of 53 HB individuals was analysed together with a sample of 40 Pura Raza Española horses for comparison....
Substitution of human for horse urine disproves an accusation of doping*. In order to detect switching and/or manipulation of samples, the owner of a stallion asked our lab to perform a DNA test on a positive doping urine sample. The objective was to compare the urine DNA profile versus blood and hair DNA profiles from the same stallion. At first, 10 microsatellite markers were investigated to determine the horse identity. No results were obtained when horse specific markers were typed in the urine sample. In order to confirm the species origin of this sample we analyzed the mitochondrial cytochrome b gene. This analysis from blood and hair samples produced reproduc...
Genetic diversity and admixture analysis of Sanfratellano and three other Italian horse breeds assessed by microsatellite markers. Sanfratellano is a native Sicilian horse breed, mainly reared in the north east of the Island, developed in the 19th century from local dams and sires with a restricted introgression of Oriental, African and, more recently, Maremmano stallions. In this study, the genetic relationships and admixture among Sanfratellano, the other two Sicilian autochthonous breeds and Maremmano breed were assessed using a set of microsatellites. The main goals were to infer the impact of Maremmano breed in the current Sanfratellano horse and to provide genetic information useful to improve the selection strategi...
Genetic diversity in the Pantaneiro horse breed assessed using microsatellite DNA markers. The genetic variability for a sample of 227 animals from three populations of Pantaneiro horses was estimated using data from 10 microsatellite loci. The number of alleles and the proportion of heterozygosity indicated high variability. A total of 91 alleles were found, with a significantly high mean number of alleles. The mean polymorphic information content was 0.7 and the paternity exclusion probability was 99.3%. The inbreeding coefficient (F(IS)) was low for the three populations: Ipiranga (F(IS) = 0.147), Nova Esperança (F(IS) = 0.094) and Promissão (F(IS) = 0.108). Genetic differentia...
Associations between candidate gene markers at a quantitative trait locus on equine chromosome 4 responsible for osteochondrosis dissecans in fetlock joints of South German Coldblood horses. A previously accomplished whole-genome scan for osteochondrosis (OC) and OC dissecans (OCD) in South German Coldblood horses using 250 microsatellite markers identified putative quantitative trait loci (QTL). A chromosome-wide significant QTL for fetlock OCD was found on Equus caballus chromosome (ECA) 4q at a relative position of 70.0-73.3 cM. The aim of this study was to analyze associations of single nucleotide polymorphisms (SNPs) in candidate genes for OC in this region. The association analysis included 32 affected and 64 unaffected horses. Three SNPs located in intron 8, intron 9, and 3...
Biochemical and genetic evaluation of the role of AMP-activated protein kinase in polysaccharide storage myopathy in Quarter Horses. To evaluate whether biochemical or genetic alterations in AMP-activated protein kinase (AMPK) play a role in the development of polysaccharide storage myopathy (PSSM) in Quarter Horses. Methods: 30 PSSM-affected and 30 unaffected (control) Quarter Horses. Methods: By use of an established peptide phosphotransfer assay, basal and maximal AMPK activities were measured in muscle biopsy samples obtained from 6 PSSM-affected and 6 control horses. In 24 PSSM-affected and 24 control horses, microsatellite markers identified from the chromosomal locations of all 7 AMPK subunit genes were genotyped wit...
Genome-wide search for markers associated with osteochondrosis in Hanoverian warmblood horses. A genome-wide scan was performed to detect quantitative trait loci (QTLs) for osteochondrosis (OC) and osteochondrosis dissecans (OCD) in horses. The marker set comprised 260 microsatellites. We collected data from 211 Hanoverian warmblood horses consisting of 14 paternal half-sib families. Traits used were OC (fetlock and/or hock joints affected), OCD (fetlock and/or hock joints affected), fetlock OC, fetlock OCD, hock OC, and hock OCD. The first genome scan included 172 microsatellite markers. In a second step 88 additional markers were chosen to refine putative QTLs found in the first scan....
Genetic diversity in a feral horse population from Sable Island, Canada. 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...
Population sub-structuring among Trypanosoma evansi stocks. To investigate the population genetic structure of Trypanosoma evansi from domesticated animals, we have analysed 112 stocks from camels, buffaloes, cattle and horses using the tandemly repeated coding sequence (MORF2) and minisatellite markers 292 and cysteine-rich acidic integral membrane protein (CRAM). We recorded a total of six alleles at the MORF2 locus, seven at 292 and 12 at the CRAM loci. Nei's genetic distance showed reduced allelic diversity between buffaloes and cattle stocks (1.2) as compared to the diversity between camels and buffaloes (3.75) and camels and cattle stock (1.69). ...
Mapping quantitative trait loci for osteochondrosis in fetlock and hock joints and palmar/plantar osseus fragments in fetlock joints of South German Coldblood horses. The aim of this study was to identify quantitative trait loci (QTL) for osteochondrosis (OC) and palmar/plantar osseous fragments (POF) in fetlock joints in a whole-genome scan of 219 South German Coldblood horses. Symptoms of OC and POF were checked by radiography in 117 South German Coldblood horses at a mean age of 17 months. The radiographic examination comprised the fetlock and hock joints of all limbs. The genome scan included 157 polymorphic microsatellite markers. All microsatellite markers were equally spaced over the 31 autosomes and the X chromosome, with an average distance of 17.7...
Genome-wide search for microsatellite markers associated with radiologic alterations in the navicular bone of Hanoverian warmblood horses. The aim of this study was to identify quantitative trait loci (QTLs) for pathologic changes in the navicular bone in Hanoverian warmblood horses. Seventeen paternal half-sib groups comprising 192 individuals were analyzed in a whole-genome scan. These families included 144 progeny and grandchildren, which were randomly chosen from the Hanoverian warmblood. Three different traits were considered: deformed canales sesamoidales and radiographic changes in the contour and in the structure of the navicular bone. The genome scan included in total 214 highly polymorphic microsatellite markers. The pu...
A case of multiple assignments (paternity/maternity) in an equine-out breeding system. Recently, the use of DNA markers has provided a more accurate method of identifying individuals and verifying parentage. In this report, we describe foal assignment in a farm bred jumping horses (Silla argentino). Ten mares were freely served by two stallions, resulting in nine foals. Weaning occurred without registration of the mare of each offspring, resulting in a failure to identify either the mare or the sire of each foal. Animals were typed using 12 microsatellite systems and four biochemical polymorphisms in order to determine the paternity/maternity of each foal. We used the CERVUS pro...
A region on equine chromosome 13 is linked to recurrent airway obstruction in horses. REASONS FOR STUDY: Equine recurrent airway obstruction (RAO) is probably dependent on a complex interaction of genetic and environmental factors and shares many characteristic features with human asthma. Interleukin 4 receptor a chain (IL4RA) is a candidate gene because of its role in the development of human asthma, confirmation of this association is therefore required. Methods: The equine BAC clone containing the IL4RA gene was localised to ECA13q13 by the FISH method. Microsatellite markers in this region were investigated for possible association and linkage with RAO in 2 large Warmblood ...
Bottleneck study and genetic structure of Iranian Caspian horse population using microsatellites. Genetic diversity within the Iranian Caspian horse was evaluated using 8 different microsatellite pairs on 45 Caspian horse blood samples. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks, if any, in this breed. The number of alleles per locus varied from 3 to 5 with mean value of 4.125. All markers have relatively high PIC value (> 0.6), observed heterozygosity; 0.9433, expected Levene's heterozygosity 0.6856 and expected Nei's heterozygosity equal to 0.6762. This study indicated the existence of substantial genetic diversity in the Caspian hors...
Genetic relationships of five Indian horse breeds using microsatellite markers. The genetic relationships of five Indian horse breeds, namely Marwari, Spiti, Bhutia, Manipuri and Zanskari were studied using microsatellite markers. The DNA samples of 189 horses of these breeds were amplified by polymerase chain reaction using 25 microsatellite loci. The total number of alleles varied from five to 10 with a mean heterozygosity of 0.58 ± 0.05. Spiti and Zansakari were the most closely related breeds, whereas, Marwari and Manipuri were most distant apart with Nei's DA genetic distance of 0.071 and 0.186, respectively. In a Nei's DA genetic distances based neighbour joining...
Inbreeding and genetic structure in the endangered Sorraia horse breed: implications for its conservation and management. 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...
Molecular genetic analysis of the ATP2A2 gene as candidate for chronic pastern dermatitis in German draft horses. Chronic pastern dermatitis predominantly affects draft horses, and this condition is characterized by hyperkeratotic-hyperplastic dermal alterations. Chronic pastern dermatitis resembles the acral-hemorrhagic phenotype of Darier-White disease in humans. The ATP2A2 gene has been shown to be responsible for human Darier-White. Thus, we chose ATP2A2 on equine chromosome 8 (ECA8) as candidate for chronic pastern dermatitis in coldblood horses. A linkage analysis was performed in 10 paternal half-sib families consisting of 85 German coldblood horses using a microsatellite closely linked to ATP2A2, ...
Whole-genome linkage disequilibrium screening for complex traits in horses. The identification of candidate genes for significant traits is crucial. In this study, we developed and tested effective and systematic methods based on linkage disequilibrium (LD) for the identification of candidate regions for genes with Mendelian inheritance and those associated with complex traits. Our approach entailed the combination of primary screening using pooled DNA samples based on DeltaTAC, secondary screening using an individual typing method and tertiary screening using a permutation test based on the differences in the haplotype frequency between two neighbouring microsatellit...
Molecular analysis using mitochondrial DNA and microsatellites to infer the formation process of Japanese native horse populations. To assess the genetic diversity of Japanese native horse populations, we examined seven such populations using mitochondrial DNA (mtDNA) and microsatellite analyses. Four reference populations of Mongolian horses and European breeds were employed as other equids. In the mtDNA analysis, the control region (D-loop) of 411 bp was sequenced, and 12 haplotypes with 33 variable sites were identified in the Japanese native horses. The phylogenetic tree constructed by haplogrouping and using worldwide geographic references indicated that the haplotypes of the Japanese native horses were derived from s...
Genetic diversity and relationships of Portuguese and other horse breeds based on protein and microsatellite loci variation. There are three native Portuguese horse breeds: Lusitano, Sorraia and Garrano. This study compares diversity patterns of 17 protein and 12 microsatellite markers in these three as well as 30 other breeds to infer relationships among the breeds and to compare levels of polymorphism of these breeds for use in conservation efforts. The Garrano and the Lusitano showed a high level of genetic diversity, similar to that observed for most of the other analysed breeds, while the Sorraia and Friesian breeds showed low levels of variation for both genetic marker types. The combined protein and microsate...
Improved resolution of the comparative horse-human map: investigating markers with in silico and linkage mapping approaches. Genetic maps are extremely important tools for tracing the genes that govern economically significant traits, and microsatellites are a significant component of these. In this study, we isolated 2346 novel horse microsatellites as resources for the construction of high-density horse genetic maps. Of these 2346 markers, 339 (14.5%) horse sequences showed sequence homology to DNA sequences in the human genome, demonstrating that microsatellites as type II markers are valuable resources for developing linkage maps and that they have a potential equal to that of type I markers for developing compa...
Molecular and cytogenetic paternity testing of a male offspring of a hinny. An alleged male foal of a female mule, whose sire and grandparents were unknown, was identified for its pedigree. Parentage testing was conducted by comparing polymorphism of 12 microsatellite DNA sites and mitochondrial D-loop sequences of the male foal and the female mule. Both the sequence analysis of species-specific DNA fragments and a cytogenetic analysis were performed to identify the species of the foal and its parents. The results showed that the alleged female mule is actually a hinny, and the male foal, which possesses 62 chromosomes, qualifies as an offspring of the female hinny an...
Genetic structure and phylogenetic relationships of the Polish Heavy horse. In this study a wide range of genetic markers (12 microsatellites, 7 blood-group loci, 10 blood-protein loci) and mitochondrial DNA (mtDNA) were used to assess genetic diversity in Polish Heavy horses. Three random samples were sequenced for 421 bp of the mitochondrial D-loop region, but no clear phylogenetic patterns were seen in mtDNA variation. Both heterozygosity and diversity levels are fairly high in Polish Heavy horses. In phylogenetic analysis the draught horses form a distinct cluster that pairs with the true pony breeds. Within this 'cold-blooded' group, the Polish Heavy Horse cluste...
Saving feral horse populations: does it really matter? A case study of wild horses from Doñana National Park in southern Spain. In the 1980s, a conservation programme involving a feral horse population, the Retuertas horses from the Guadalquivir marshes, was started in the Doñana National Park. The analysis of an extensive genetic survey of this population, which now numbers 100 animals, and 10 additional European and North African breeds using DNA polymorphisms from 22 microsatellites is presented. Highly significant fixation indexes were obtained for all pairwise comparisons between the Retuertas population and other breeds. A population neighbour-joining breed phenogram was built using different distance measures, ...