Genetic diversity in the modern horse illustrated from genome-wide SNP data.

Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity.

Genome-wide analysis reveals selection for important traits in domestic horse breeds.

Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.

A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies.

An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.

Genetic characterization of the endangered Kiso horse using 31 microsatellite DNAs.

In order to contribute to conservation of the endangered Kiso horse, we clarified their genetic information using 31 microsatellite DNAs, and genotyped 125 horses, 83% of the existing breed. First, we clarified the current status of the horses. The horses were confirmed to have experienced rapid loss of population causing a bottleneck, and their effective population size was much smaller than their census size.

Population statistics and biological traits of endangered kiso horse.

The objective of this study was to clarify the current status of endangered Kiso horse, population statistics and biological traits, in order to take a step for the conservation by scientific approach. We surveyed 125 Kiso horses (86.2% of the whole breed), analyzed the construction of the population, and calculated the coefficient of inbreeding and effective population size.

Construction and validation of parentage testing for thoroughbred horses by 53 single nucleotide polymorphisms.

We characterized the SNP 53 JPN System for parentage verification during horse registry. The SNP 53 JPN System was constructed using 53 highly polymorphic single nucleotide polymorphisms (SNPs), which were amplified and genotyped with 2 multiplex assays. The SNP 53 JPN System showed good resolution for 95 unrelated thoroughbreds, and the exclusion probability (PE01) for each SNP ranged from 11.

Gene dropping analysis of ancestral contributions and allele survival in Japanese thoroughbred population.

Genetic contributions of nine historically important ancestors and allelic diversity in the Japanese Thoroughbred population were examined by applying the gene dropping simulation to the foals produced from 1978 to 2005. Full pedigree records traced to ancestors (base animals) born around 1890 were used for the simulation. Alleles originated from some of the historically important ancestors were found to be at risk of future extinction, although their genetic contributions to the foal population have increased during the last three decades.

Demographic analysis of breeding structure in Japanese thoroughbred population.

To investigate the breeding structure in the Japanese Thoroughbred population, we applied a demographic analysis to the populations of foals produced from 1978 to 2005. The migration rate estimated from the proportion of foals produced by imported breeding horses was around 40% over the investigated period. After early 1990s, the migration rate through stallions imported from USA sharply increased.

Type VII and XVII Collagen mRNA Expressions in Regenerated Epidermal Laminae in Chronic Equine Laminitis.

To confirm ability forming the basement membrane of the regenerated laminar epidermis (rLE) in chronic laminitis, expression of type VII and type XVII collagen mRNAs in the rLE was studied applying sequences of two type of murine collagens. On northern blot analysis, complement DNA (cDNA) probes adjusted from the murine type VII and type XVII collagen could hybridize with the equine mRNAs, and each signal was detected as single-bands at approximately 9.5 kb and 5.

Estimation models for the morbidity of the horses infected with equine influenza virus.

Estimation formulas for the morbidity of horses infected with equine influenza virus by linear regression, logistic regression and probit transformation were developed, using data from the outbreak at the Sha Tin Racing Track in Hong Kong in 1992. Using these formulas, we estimated the equine influenza virus morbidity rates at training centers belonging to the Japan Racing Association (JRA) in October 1997 and in October 1998. In 1998 JRA started a new vaccination program, and every horse must now be vaccinated twice per year.

In vitro development of equine oocytes from preserved ovaries after intracytoplasmic sperm injection.

In this study, we evaluated the meiotic competence of equine oocytes from ovaries preserved for one day. We also investigated fertilization, cleavage rate, developmental competence and freezability of equine embryos after intracytoplasmic sperm injection (ICSI). After collection from ovaries, the oocytes were classified into two groups comprised of those having compact cumulus layers (Cp) or those having expanded cumulus layers (Ex).

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 microsatellites.

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.

Polymorphism identification, RH mapping, and association analysis with the anxiety trait of the equine serotonin transporter (SLC6A4) gene.

Equine anxiety trait is considered an important temperament in various situations, including riding, training, and daily care. This study examined the polymorphism of the equine serotonin transporter (SLC6A4) gene as a candidate genetic element influencing equine anxiety trait. The sequence of the coding region of this gene was highly homologous with those of other mammals, and four single nucleotide polymorphisms were found by comparing the sequences of ten genetically unrelated thoroughbred horses.

Single linkage group per chromosome genetic linkage map for the horse, based on two three-generation, full-sibling, crossbred horse reference families.

A genetic linkage map of the horse consisting of 742 markers, which comprises a single linkage group for each of the autosomes and the X chromosome, is presented. The map has been generated from two three-generation full-sibling reference families, sired by the same stallion, in which there are 61 individuals in the F2 generation. Each linkage group has been assigned to a chromosome and oriented with reference to markers mapped by fluorescence in situ hybridization.

Prospects for whole genome linkage disequilibrium mapping in thoroughbreds.

Linkage disequilibrium (LD) mapping is often used in searches for genes governing economically significant traits and diseases. The D' coefficient is a commonly used measure of the extent of LD between all possible pairs of alleles at two markers. This study aimed to test the utility of the D' coefficient for LD mapping of a trait in a thoroughbred population.

Nucleotide sequence of equine erythropoietin and characterization of region-specific antibodies.

Objective: To determine the full-length complementary DNA (cDNA) sequence of equine erythropoietin (EPO) and to develop region-specific antibodies to differentiate equine EPO (eEPO) and human EPO (hEPO).

Sample Population: RNA and lysate extracted from renal tissues of an adult Thoroughbred.

Procedure: Full-length cDNA was determined by use of a reverse transcriptase-polymerase chain reaction assay and a rapid amplification of cDNA ends method.

Molecular cloning, nucleotide sequence and presence of multiple functional polyadenylation signals in the 3'-untranslated region of equine dopamine beta-hydroxylase cDNA.

Complementary DNA (cDNA) encoding equine dopamine beta-hydroxylase (DBH) was amplified with a combination of reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) method, and their nucleotide sequences (Accession No. AB029430: the DDBJ nucleotide sequence database) was determined. A total of 3842 bp cDNA sequence was consisted with 5 bp of 5' flanking untranslated sequence, 1833 bp of open reading frame encoding 610 amino acids, and 2004 bp of 3' flanking untranslated sequence.

Immunohistochemical localization of chromogranin a in the acinar cells of equine salivary glands contrasts with rodent glands.

We investigated the existence of chromogranin A (CgA) in salivary glands of the horse by Western blotting and enzyme immunoassay (EIA) using an antiserum against a peptide sequence of equine CgA. We also compared its cellular distribution between the horse and rat salivary glands with a tyramide signal amplification immunofluorescence technique. Western blotting gave three significant immunoreactive bands (74, 56 and 48 kDa) in adrenal medulla and three major salivary glands of horses.

Determination of nitrotyrosine by HPLC-ECD and its application.

3-nitrotyrosine, a product of tyrosine nitration, is a useful indicator of oxidative damage. We modified the previously reported HPLC-electrochemical detection (ECD) method: specifically, a through-type porous carbon electrode was used as a reducing electrode instead of the mercury-gold amalgam electrode, because the response of the latter changes over time. A combination of reverse-phase HPLC and electrochemical detector passed through -800 mV reduction potential and subsequently under +250 mV oxidation potential allows measurement of 3-nitrotyrosine.