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.
Shiue YL, Bickel LA, Caetano AR, Millon LV, Clark RS, Eggleston ML, Michelmore R, Bailey E, Guérin G, Godard S, Mickelson JR, Valberg SJ, Murray JD....To generate a domestic horse genome map we integrated synteny information for markers screened on a somatic cell hybrid (SCH) panel with published information for markers physically assigned to chromosomes. The mouse-horse SCH panel was established by fusing pSV2neo transformed primary horse fibroblasts to either RAG or LMTk mouse cells, followed by G418 antibiotic selection. For each of the 108 cell lines of the panel, we defined the presence or absence of 240 genetic markers by PCR, including 58 random amplified polymorphic DNA (RAPD) markers and 182 microsatellites. Thirty-three syntenic gr...
Gallagher PC, Lear TL, Coogle LD, Bailey E.BLAST searches of 61 equine microsatellite sequences revealed two related families of retroposons. The first family included seven markers, all of which showed significant homology to the Equine Repetitive Element-1 (ERE-1) Short Interspersed Nucleotide Element (SINE) sequence. Length of homology ranged from 76 to 171 bases with identities to the ERE-1 consensus sequence ranging from 71% to 83%. The second family referred to as Equine Repetitive Element-2 (ERE-2) has a consensus sequence that showed homology to ERE-1 over approximately 60 bases. These 60 bases comprised subunit I. Sequence com...
Glazko VI, Oblap RV, Iasinetskaia NA, Kushnir AN.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.
Horín P, Cothran EG, Trtková K, Marti E, Glasnák V, Henney P, Vyskocil M, Lazary S.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...
Lindgren G, Sandberg K, Persson H, Marklund S, Breen M, Sandgren B, Carlstén J, Ellegren H.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...
Tikhonov VN, Cothran EG, Kniazev SP.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...
Godard S, Schibler L, Oustry A, Cribiu EP, Guérin G.A horse BAC library was constructed with about 40,000 clones and mean insert size of 110 kb representing a 1.5 genome equivalent coverage and a probability of finding a single sequence of 0.75. It was characterized by PCR screening of about 130 sequences of horse microsatellites and exonic gene sequences retrieved from databases. BACs containing 8 microsatellites and 12 genes were subsequently localized by fluorescent in situ hybridization (FISH) on chromosomes. Two linkage groups were newly assigned to chromosomes: LG2 to ECA3 and LG5 to ECA24, and five linkage groups were also oriented--LG3,...
Guèrand M, Mahla R, Lagneaux D, Amigues Y, Palmer E, Bézard J.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...
Eggleston-Stott ML, Delvalle A, Dileanis S, Wictum E, Bowling AT.The equine dinucleotide microsatellite HMS7 is part of a microsatellite panel utilized in a parentage verification programme at the Veterinary Genetics Laboratory (Davis, California, USA). Apparent non-Mendelian inheritance was noted when a Quarter Horse mare was excluded as the parent of two offspring based on analysis of the HMS7 locus. The mare's DNA type qualified her as a parent of the offspring at an additional 20 microsatellite loci. The three animals appeared homozygous for HMS7 with each possessing an allele different from that of the other two animals. Polymerase chain reaction prime...
Caetano AR, Bowling AT.Insulin-like growth factor 1 (IGF1) regulates growth and metabolic functions in vertebrates. A dinucleotide repeat sequence located at the promoter region of the IGF1 gene has been reported in several vertebrate species and may affect the control of the transcriptional activity of this gene. The genotypes of animals from seven horse breeds were determined in order to study the potential association of allelic forms of this microsatellite with adult body size differences found in domestic horses. Among these breeds, five alleles were found. Breed-specific differences in adult body size could no...
Godard S, Vaiman D, Oustry A, Nocart M, Bertaud M, Guzylack S, Mériaux JC, Cribiu EP, Guérin G.Thirty-six new horse microsatellites (11 from plasmid libraries and 25 from a cosmid library) were isolated and characterized on a panel of four horse breeds. Thirty were found to be polymorphic with heterozygosity levels ranging between 0.20 and 0.87. Twenty-two of the cosmids were physically mapped to R-banded single horse Chromosomes (Chrs) 1, 3, 4, 9, 11, 12, 13, 15, 18, 19, 21, 22, 23 and three to pericentromeric regions. Furthermore, linkage analysis between a selection of 42 DNA markers, including those presented in this study, and 16 conventional markers of the horse hemotype was perfo...
Bowling AT, Eggleston-Stott ML, Byrns G, Clark RS, Dileanis S, Wictum E.A parallel testing of 4803 routine Quarter Horse parentage cases, using 15 loci of blood group and protein polymorphisms (blood typing) and 11 loci of dinucleotide repeat microsatellites (DNA typing), validated DNA markers for horse pedigree verification. For the 26 loci, taken together, the theoretical effectiveness of detecting incorrect parentage was 99.999%, making it extremely unlikely that false parentage would fail to be recognized. The tests identified incorrect parentage assignment for 95 offspring (2% of cases). Despite fewer loci, DNA typing was as effective as blood typing and, in ...
Bailey E, Reid RC, Skow LC, Mathiason K, Lear TL, McGuire TC.Equine combined immunodeficiency disease (CID) is caused by homozygosity for an autosomal recessive gene. To identify linked markers for the disease, we studied a family segregating for the equine CID gene. A stallion and 19 of his CID-affected offspring were tested for marker segregation at 23 microsatellite DNA loci. His CID-affected offspring inherited only one of his two alleles at the HTG8 and HTG4 loci, namely HTG8-186 and HTG4-124, respectively. Lod scores for linkage to the CID gene using a theta of 0.01 were 5.34 for HTG8 and 2.37 for HTG4. The apparent genotypes also suggested linkag...
Breen M, Lindgren G, Binns MM, Norman J, Irvin Z, Bell K, Sandberg K, Ellegren H.Twenty equine microsatellites were isolated from a genomic phage library, and their genetical and physical localization was sought by linkage mapping and fluorescent in situ hybridization (FISH). Nineteen of the markers were found to be polymorphic with, in most cases, heterozygosities exceeding 50%. The markers were mapped in a Swedish reference family for gene mapping, comprising eight half-sib families from Standardbred and Icelandic horse sires. Segregation was analyzed against a set of 35 other markers typed in the pedigree. Thirteen of the microsatellites showed linkage to at least one o...
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...
DeAssis JB, DeLaat DM, Peixoto MG, Bergmann JA, Fonseca CG, Carvalho MR.One hundred and fifteen unrelated Mangalarga Marchador horses were sampled from three geographically distinct regions of Minas Gerais State, Brazil (South, Southeast, and Northeast) and tested for 10 microsatellite loci. Genetic diversity and population structure parameters were estimated with ARLEQUIN 3.0, CERVUS 2.0, POPGENE 1.31, GENEPOP on the web, STRUCTURE 2.0, and SPAGEDI 1.2 software packages. Under Hardy-Weinberg assumptions, seven markers were at equilibrium (LEX014, LEX017, LEX019, SGCV23, TKY321, VHL20, and VIASH39), while two (ASB3 and LEX031) presented significant homozygote exce...
Rusek J, Klumplerova M, Molinkova D, Sedlinska M, Dusek L, Muzik J, Putnova L, Vrtkova I, Celer V, Horin P.Individual variation in immune responses to herpesviruses was observed in various species. Here, associations between polymorphic molecular markers and life-long anti-EHV-1/4 antibody immune responses were analyzed in a model EHV-infected population of the Old Kladruber horses. Two-dimensional analysis including overall mean titers and titer dynamics expressed by differences between spring and autumn titers allowed identification of low-responders. 50 randomly selected microsatellites and nine single nucleotide polymorphisms in nine immunity-related candidate genes were genotyped. Due to diffe...
Moodley Y, Baumgarten I, Harley EH.We investigated the applicability of microsatellite primers, designed in horses, for use in plains and mountain zebras. Fifteen of the 20 tested horse-isolated primer pairs reliably amplified polymorphic loci in two wild equid species. We used this information to assess whether levels of genetic variation and repeat size differed in species from which microsatellites were isolated and in closely related target species. Target equid species exhibited similar levels of genetic variation to the horse, the species from which primers were originally isolated. We show that ascertainment bias results...
Caetano AR, Bowling AT.Insulin-like growth factor 1 (IGF1) regulates growth and metabolic functions in vertebrates. A dinucleotide repeat sequence located at the promoter region of the IGF1 gene has been reported in several vertebrate species and may affect the control of the transcriptional activity of this gene. The genotypes of animals from seven horse breeds were determined in order to study the potential association of allelic forms of this microsatellite with adult body size differences found in domestic horses. Among these breeds, five alleles were found. Breed-specific differences in adult body size could no...
Rukavian D, Hasanbasic D, Ramic J, Zahirovic A, Ajanovic A, Beganovic K, Durmic-Pasic A, Kalamujic B, Pojskic N.The focus of this study was on genetic diversity of TB horse population raised in B&H. Genomic DNA was genotyped by using 17 microsatellite markers. A total of 103 alleles were detected. The average number of alleles per locus was 6.059 and effective number of alleles was 3.293. Means of observed and expected heterozygosity were calculated 0.645 and 0.696, respectively. The average PIC values was 0.649 and inbreeding coefficient was 0.090. Based on all observed parameters, ASB2 locus showed the highest genetic diversity while locus HMS2 was the least diverse. These results suggest that the pop...
Nakamura M, Tozaki T, Kakoi H, Nakamura K, Rajabi-Toustani R, Ohba Y, Matsubara T, Takasu M.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...
Bömcke E, Soyeurt H, Szydlowski M, Gengler N.Relationship coefficients are traditionally based on pedigree data. Today, with the development of molecular techniques, they are often completely replaced by coefficients calculated from molecular data. Examples are relationships from microsatellites for biodiversity studies but also genomic relationships from SNP as currently used in genomic prediction of breeding values. There are, however, many situations in which optimal combination of both sources would be the best solutions. Obviously, this is the case for incompletely genotyped populations, but also when pedigree information is sparse....
Duderstadt S, Distl O.The objectives of the present study were to analyze the influence of the stallions employed in the Dülmen wild horses on the genetic diversity and population substructure using Bayesian cluster analysis. The Dülmen wild horse is maintained as a unique horse population exposed to the natural conditions all year round in the Merfelder Bruch near Dülmen in Westphalia, Germany. Stallions selected for breeding have to prove their abilities to survive under this harsh environment. We used multilocus genotypic information from a set of 29 autosomal microsatellites to determine the paternity of 185...
The Shagya Arabian horse breed was created to address the need of Imperial Hussars (Hungarian light horsemen) for a horse with the intelligence, essential characteristics, and endurance of the Arabian breed, but also of a bigger size and having a better weight-carrying capacity and jumping ability. The present study aimed to explore the genetic variability and population structure of the uninvestigated Shagya Arabian horse population in Bulgaria based on genotyping at 15 equine microsatellite markers. A total of 140 horses belonging to six genealogical lines (Dahoman, Gazal, Ibrahim, Kuhailan ...
Bubenikova J, Plasil M, Futas J, Stejskalova K, Klumplerova M, Oppelt J, Suchentrunk F, Burger PA, Horin P.The immunogenome is the part of the genome that underlies immune mechanisms and evolves under various selective pressures. Two complex regions of the immunogenome, major histocompatibility complex (MHC) and natural killer cell receptor (NKR) genes, play an important role in the response to selective pressures of pathogens. Their importance is expressed by their genetic polymorphism at the molecular level, and their diversity associated with different types of diseases at the population level. Findings of associations between specific combinations of MHC/NKR haplotypes with different diseases i...
Glazko VI, Oblap RV, Iasinetskaia NA, Kushnir AN.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.
The Journal of heredityNovember 25, 2009
Volume 101, Issue 2 240-245 doi: 10.1093/jhered/esp090
Dobosz M, Bocci C, Bonuglia M, Grasso C, Merigioli S, Russo A, De Iuliis P.Microsatellites have been used for parentage testing and individual identification in forensic science because they are highly polymorphic and show abundant sequences dispersed throughout most eukaryotic nuclear genomes. At present, genetic testing based on DNA technology is used for most domesticated animals, including horses, to confirm identity, to determine parentage, and to validate registration certificates. But if genetic data of one of the putative parents are missing, verifying a genealogy could be questionable. The aim of this paper is to illustrate a new approach to analyze complex ...
Jaworska J, Tobolski D, Janowski T.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...
Pazdera J, Hruban V, Pichrtová J, Müller Z, Jílek F.Using a multilocus DNA probe, individual - specific hybridization patterns, the so-called DNA fingerprints (TAB) were determined in six horse families by the DNA fingerprinting method. The probe with evolutionally preserved nucleotide sequence from bacteriophage M13 determines hypervariable regions placed in genomic minisatellite DNA. The use of this probe permits an identification of an individual and execution of paternity relationships with a probability over 99.99 per cent.
Sátková-Jakabová D, Trandzík J, Hudecová-Kvasnáková L, Hegedüsová-Zetochová E, Bugarský A, Buleca J, Zöldág L, Jakab F, Fl'ak P.Genetic variation at six microsatellite loci was analysed for five Thoroughbred subpopulations to determine the magnitude of genetic differentiation and the genetic relationships among the subpopulations. Significant deviations from Hardy-Weinberg equilibrium were shown for a number of locus-population combinations, with all subpopulations. The genetic diversities and relationships of five Thoroughbred subpopulations were evaluated using six microsatellites recommended by the International Society of Animal Genetics (ISAG). The allele frequencies, the effective numbers of alleles, and the obse...
