Topic:Genotyping
Genotyping in horses involves analyzing the genetic makeup of individual horses to identify specific genetic markers. This process aids in understanding genetic variations that may influence traits such as coat color, disease susceptibility, and performance capabilities. Genotyping can be used in breeding programs to select for desirable traits and manage genetic diversity within populations. Common methods for genotyping include single nucleotide polymorphism (SNP) analysis and microsatellite markers. This page compiles peer-reviewed research studies and scholarly articles that explore the methodologies, applications, and implications of genotyping in equine genetics and breeding.
The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data. Partition of the genetic variability, genetic structure and relationships among seven Spanish Celtic horse breeds were studied using PCR amplification of 13 microsatellites on 481 random individuals. In addition, 60 thoroughbred horses were included. The average observed heterozygosity and the mean number of alleles were higher for the Atlantic horse breeds than for the Balearic Islands breeds. Only eight percentage of the total genetic variability could be attributed to differences among breeds (mean FST approximately 0.08; P < 0.01). Atlantic breeds clearly form a separate cluster from th...
Determination of intraspecies variations of the V2 region of the 16S rRNA gene of Streptococcus equi subsp. zooepidemicus. The 16S rRNA gene of 39 S. equi subsp. zooepidemicus strains and two S. equi subsp. equi strains was amplified by polymerase chain reaction and subsequently digested with the restriction enzyme Hinc II. A restriction profile with two fragments with sizes of 1250 bp and 200 bp could be observed for both S. equi subsp. equi strains and for 30 of the 39 S. equi subsp. zooepidemicus strains indicating a sequence variation within the V2 region of the 16S rRNA gene of the remaining nine S. equi subsp. zooepidemicus isolates. A segment of the 16S rRNA gene including the hypervariable V2 region of 11 ...
Comparison of the phenotypes of Streptococcus zooepidemicus isolated from tonsils of healthy horses and specimens obtained from foals and donkeys with pneumonia. To determine whether streptococcal pneumonia is caused by strains of Streptococcus zooepidemicus similar to those obtained from the tonsils of healthy horses. Methods: 5 tonsils from healthy horses, 8 tracheal washes and 6 lung specimens from foals with pneumonia, and 5 nasopharyngeal swab specimens from donkeys with acute bronchopneumonia. Methods: Variable M-like protectively immunogenic SzP proteins of 5 isolates of S. zooepidemicus from each tonsil and clinical specimen were compared, using immunoblots. The SzP gene of 13 isolates representative of various SzP immunoblot phenotypes from 1 ...
Mitochondrial D-loop sequence variation among the 16 maternal lines of the Lipizzan horse breed. Mitochondrial DNA from 49 Lipizzan horses representing 16 maternal lines from the original stud at Lipica was used for SSCP analysis and DNA sequencing. The SSCP analysis of the 444 bp long fragment of the D-loop region extending from the tRNA(Pro) gene to the central conserved sequence block revealed three distinct groups of SSCP patterns. Both ends of the D-loop region (378 bp and 310 bp), which are considered as the most variable regions within the mammalian mitochondrial DNA, were sequenced. According to 49 polymorphic sites identified within the both parts of the D-loop region, the 16 mat...
Report of the International Equine Gene Mapping Workshop: male linkage map. The goal of the First International Equine Gene Mapping Workshop, held in 1995, was the construction of a low density, male linkage map for the horse. For this purpose, the International Horse Reference Family Panel (IHRFP) was established, consisting of 12 paternal half-sib families with 448 half-sib offspring provided by 10 laboratories. Blood samples were collected and DNA extracted in each laboratory and sent to the Lexington laboratory (KY, USA) for dispatch in aliquots to 14 typing laboratories. In total, 161 markers (144 microsatellites, seven blood groups and 10 proteins) were tested f...
Detection of a common genotype among strains of Taylorella equigenitalis isolated from thoroughbred horses in Japan between 1994 and 1996. We examined whether or not the genotype J could be detected among 21 new strains of T. equigenitalis isolated between 1994 and 1996 in Japan since our previous report (MIYAZAWA et al. 1995). The respective pulsed-field gel electrophoretic profiles of the 21 Japanese strains, as well as those of an old EQ59 used as a reference strain after separate digestion with the two restriction enzymes, ApaI and NotI, were essentially identical but differed from those of T. equigenitalis NCTC11184T and KENTUCKY 188, respectively. Hence, the 21 strains and EQ59 appeared to have a common genotype J. Conseque...
Genetic analysis of three South African horse breeds. Genetic variability at 7 blood-group and 10 biochemical genetic loci was examined in 3 South African horse breeds, the Nooitgedacht, Boerperd and Basuto Pony. Observed heterozygosity for these breeds was intermediate for domestic horses, with the highest heterozygosity in the Boerperd and the lowest in the Basuto Pony. The 3 breeds show greater genetic similarity to each other than to other domestic horse breeds. Compared to other breeds, the South African breeds show greater genetic similarity to breeds such as the Thoroughbred, Holstein, Trakehner and Hanovarian and also to North American br...
Diversity of isolates of Rhodococcus equi from Australian thoroughbred horse farms. Pulsed field gel electrophoresis of restriction endonuclease digested genomic DNA from a collection of clinical isolates of Rhodococcus equi was used to compare strain diversity on different Thoroughbred horse farms over time. Restricted diversity was found among the isolates tested, as the same strains were detected on multiple farms and in multiple years. Marked variation occurred in strain prevalence with some strains being represented by single isolates, and the most prevalent by 26 isolates. There were dominant strains on some farms and the prevalence of some strains differed between farm...
Close association between sequence polymorphism in the KIT gene and the roan coat color in horses. The roan coat color in horses is controlled by a dominant allele that is lethal in the homozygous condition. Phenotypic similarities to some pigmentation disorders in human and mouse, combined with comparative mapping data, identified KIT, encoding the mast cell growth factor receptor, as a major candidate gene for the roan locus (Rn). Rn has previously been mapped to equine linkage group (LG) II. In this study, LGII was expanded with KIT and PDGFRA (platelet-derived growth factor receptor alpha) by use of RFLP and linkage analysis. Moreover, highly significant linkage disequilibrium between R...
[The intraspecific differentiation of Przhewalski’s horse and the domestic horse by 5 molecular genetic markers]. Analysis of albumin, transferrin, receptor to vitamin D, esterase, alpha 1-beta glycoprotein polymorphisms in Przhewalski's horse, Orlov's and Russian trotters, Guzul and Yakutian domestic horse breeds was carried out. The data about similarity of intraspecies differentiation of Przewalski's horse's populations and interbreed distinctions were obtained. Locus-specific particularities of genetic structures of investigated animal groups were revealed.
Enterotoxigenic Clostridium perfringens type A necrotic enteritis in a foal. A Thoroughbred-Quarter Horse crossbred foal developed hemorrhagic enteritis and died < 48 hours after birth. Gross and histologic findings were suggestive of Clostridium perfringens type C infection, and large numbers of C perfringens were isolated from intestinal contents. However, genotyping of isolates indicated that they were enterotoxigenic C perfringens type A, and isolates were found to produce C perfringens enterotoxin in vitro. This case suggests that enterotoxigenic C perfringens type A may cause enteric disease in horses.
Polymorphism of Old Kladruber horses, a surviving but endangered baroque breed. Analysis of MHC class I and class II polymorphism, as well as data from other polymorphic systems (non-MHC lymphocyte alloantigen, blood groups systems, biochemical polymorphisms and microsatellite loci), was used to characterize the extent and distribution of the genic polymorphism of Kladruber horses. A breed-characteristic distribution of the MHC polymorphism was found. The repertoire of defined MHC class I specificities was restricted, especially in the grey subpopulation and in stallions, but a high frequency of blanks suggests the possible existence of undetected specificities. Despite t...
Phenytoin alters transcript levels of hormone-sensitive lipase in muscle from horses with hyperkalemic periodic paralysis. In equine hyperkalemic periodic paralysis (HyperPP), there is evidence suggesting that the primary defect in the sodium channel is associated with a secondary alteration in triacylglycerol-associated fatty acid metabolism (TAFAM) in skeletal muscle. Furthermore, TAFAM may be involved in the therapeutic action of phenytoin. The effects of phenytoin treatment on the transcript levels of three key proteins in TAFAM, hormone sensitive lipase (HSL), carnitine palmitoyltransferase (CPT), and fatty acid binding protein (FABP), were examined. These transcripts were quantitated by competitive reverse t...
A primary male autosomal linkage map of the horse genome. A primary male autosomal linkage map of the domestic horse (Equus caballus) has been developed by segregation analysis of 140 genetic markers within eight half-sib families. The family material comprised four Standardbred trotters and four Icelandic horses, with a total of 263 offspring. The marker set included 121 microsatellite markers, eight protein polymorphisms, five RFLPs, three blood group polymorphisms, two PCR-RFLPs, and one single strand conformation polymorphism (SSCP). One hundred markers were arranged into 25 linkage groups, 22 of which could be assigned physically to 18 different...
[Differentiation of domestic horse and Przewalskis horse using various DNA sequences]. The electrophoretic mobility of seven erythrocyte enzymes and spectra of fragments amplified by RAPD-PCR with primers UBC-85 and UBC-126 were comparatively analyzed in domestic horse and Przewalski's horse. All tested genetic markers were classified into two groups differing in their involvement in differentiation of the two closely related horse species. Markers from different groups differed neither in their type (a polymorphic protein or an amplification product) nor in their biochemical role (for enzymes).
[Population genetic parameters of aboriginal Yakut horses as related to modern breeds of the domestic horse Equus caballus L]. This study was the first to analyze the polymorphic characteristics of a wide range of biochemical markers in aboriginal Yakut horses. A total of 124 alleles, including 48 alleles of seven blood-group loci and 76 alleles of ten loci for enzymes and other proteins, were studied. For these polymorphic systems, a computer analysis of the genetic distances between 85 horse breeds of different origin from all parts of the world was performed. The low level of hereditary variation in the Yakut horses confirmed that this breed is old and has long been an isolated population. Phylogenetic analysis dem...
Diversity among isolates of Actinobacillus equuli and related organisms as revealed by ribotyping. The objective of this work was to examine the diversity within Australian isolates of Actinobacillus equuli and related organisms by the genotypic method of ribotyping. Methods: Ribotyping, performed using the enzyme HaeIII, was used to examine the diversity in 12 field isolates of A equuli (five being capable of fermenting L-arabinose), one field isolate of Pasteurella caballi and two unclassifiable field isolates. Isolates were obtained from Australian horses, except for three isolates of A equuli (one L-arabinose positive and two L-arabinose negative) which were obtained from horses and a p...
Molecular analysis of the virulence determinants of Clostridium perfringens associated with foal diarrhoea. During an epidemiological study of foal diarrhoea, over half of the cases yielded Clostridium perfringens which was significantly associated with disease (Netherwood et al., 1996b). However, the association could not be accounted for by enterotoxigenic isolates which had a low prevalence (Netherwood et al., 1997). Nonetheless, we have hypothesized that the association may be caused by a pathogenic sub-population which would be significantly more common amongst C. perfringens-positive cases compared with C. perfringens-positive healthy controls if it acted as a pathogen when present. Conversely...
Enterocolitis associated with Clostridium perfringens infection in neonatal foals: 54 cases (1988-1997). To identify clinical signs, physical examination findings, results of diagnostic tests, treatments administered, and clinical outcome of neonatal foals with enterocolitis associated with Clostridium perfringens infection. Methods: Retrospective study. Methods: 54 neonatal foals. Results: Most foals had acute onset of obtunded mentation, colic, or diarrhea and developed leukopenia, neutropenia, an abnormally high number of band neutrophils, toxic WBC, and hypoproteinemia within 24 hours after admission, despite high serum IgG concentrations (> 800 mg/dl). Abdominocentesis and abdominal radiogra...
Comparisons of three probability formulae for parentage exclusion. Three general formulae calibrate the average capability of marker systems to dispute falsely reported pedigree records in uniparous species. The most familiar exclusion formula applies to paternity, although the same formula applies equally to maternity. Another formula faults the relationship of a single offspring with its putative parent; for example, where the genotype of the other parent is not available. The remaining formulae excludes both of the falsely recorded parents of a substituted offspring. Simplified forms of the three general formulae facilitate the calculation of maximal avera...
Parentage testing of Day 10 equine embryos by amplified PCR analysis of microsatellites. Paternity analysis was performed on the DNA of 21 equine embryos collected nonsurgically 10 days after ovulation from known mares, but involving 3 possible sires. After extraction, the DNA of each embryo was typed by radioactive PCR amplification using 10 characterised microsatellites; HMS 1, 2, 5, 6, 7 and 8 (Guérin et al. 1994) and HTG 3, 4, 6 and 10 (Marklund et al. 1994). The 21 dams and 3 sires were genotyped using DNA extracted from blood and amplified by PCR. After electrophoresis and autoradiography of the PCR products of the embryo and parents, the alleles of the embryo were compared...