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Thoroughbred horses are seasonal mating animals, and their foals are born yearly in spring seasons. In northern regions or countries, the foals generally show a typical seasonal compensatory growth pattern, where their growth rate declines in winter and increases in the next spring. In this study, a new empirical approach is proposed to adjust for this compensatory growth when growth curve equations are estimated, by using BW of Japanese Thoroughbred colts and fillies raised in Hidaka, Hokkaido. Based on the traditional Richards growth curve equation, new growth curve equations were developed and fit to the weight-age data. The foals generally experience 2 major winter seasons before their debut in horseracing. The new equations had sigmoid subfunctions that can empirically adjust the first and second year compensatory growths, combined with the Richards biological parameter responsible for the maturity of animals. The unknown parameters included in the equations were estimated by SAS NLMIXED procedure. The goodness-of-fit was examined by using several indices of goodness-of-fit (i.e., Akaike's information criterion, Bayesian information criterion, -2 log likelihood, and residual sum of squares) for the multiple applications of the subfunctions. The indices indicated the best fit of the new equations including both subfunctions for the first and second compensatory growths to the weight-age data. The shapes of the growth curves were improved during the periods of compensatory growth. The proposed method is one of the useful approaches for adjusting multiple seasonal compensatory growths in growth curve estimations of Thoroughbreds and for the management of young horses during the compensatory periods.

Thoroughbred horses are seasonal mating animals, and their foals are born yearly in spring seasons. In northern regions or countries, the foals generally show a typical seasonal compensatory growth pattern, where their growth rate declines in winter and increases in the next spring. In this study, a new empirical approach is proposed to adjust for this compensatory growth when growth curve equations are estimated, by using BW of Japanese Thoroughbred colts and fillies raised in Hidaka, Hokkaido. Based on the traditional Richards growth curve equation, new growth curve equations were developed and fit to the weight-age data. The foals generally experience 2 major winter seasons before their debut in horseracing. The new equations had sigmoid subfunctions that can empirically adjust the first and second year compensatory growths, combined with the Richards biological parameter responsible for the maturity of animals. The unknown parameters included in the equations were estimated by SAS NLMIXED procedure. The goodnessof- fit was examined by using several indices of goodnessof- fit (i.e., Akaike's information criterion, Bayesian information criterion, -2 log likelihood, and residual sum of squares) for the multiple applications of the subfunctions. The indices indicated the best fit of the new equations including both subfunctions for the first and second compensatory growths to the weight-age data. The shapes of the growth curves were improved during the periods of compensatory growth. The proposed method is one of the useful approaches for adjusting multiple seasonal compensatory growths in growth curve estimations of Thoroughbreds and for the management of young horses during the compensatory periods. [PUBLICATION ABSTRACT]

A comprehensive second-generation whole genome radiation hybrid (RH II), cytogenetic and comparative map of the horse genome (2n = 64) has been developed using the 5000rad horse × hamster radiation hybrid panel and fluorescence in situ hybridization (FISH). The map contains 4,103 markers (3,816 RH; 1,144 FISH) assigned to all 31 pairs of autosomes and the X chromosome. The RH maps of individual chromosomes are anchored and oriented using 857 cytogenetic markers. The overall resolution of the map is one marker per 775 kilobase pairs (kb), which represents a more than five-fold improvement over the first-generation map. The RH II incorporates 920 markers shared jointly with the two recently reported meiotic maps. Consequently the two maps were aligned with the RH II maps of individual autosomes and the X chromosome. Additionally, a comparative map of the horse genome was generated by connecting 1,904 loci on the horse map with genome sequences available for eight diverse vertebrates to highlight regions of evolutionarily conserved syntenies, linkages, and chromosomal breakpoints. The integrated map thus obtained presents the most comprehensive information on the physical and comparative organization of the equine genome and will assist future assemblies of whole genome BAC fingerprint maps and the genome sequence. It will also serve as a tool to identify genes governing health, disease and performance traits in horses and assist us in understanding the evolution of the equine genome in relation to other species.

A comprehensive male linkage map was generated by adding 359 new, informative microsatellites to the International Equine Gene Map half-sibling reference families and by combining genotype data from three independent mapping resources: a full sibling family created at the Animal Health Trust in Newmarket, United Kingdom, eight half-sibling families from Sweden and two half-sibling families from the University of California, Davis. Because the combined data were derived primarily from half-sibling families, only autosomal markers were analyzed. The map was constructed from a total of 766 markers distributed on the 31 equine chromosomes. It has a higher marker density than that of previously reported maps, with 626 markers linearly ordered and 140 other markers assigned to a chromosomal region. Fifty-nine markers (7%) failed to meet the criteria for statistical evidence of linkage and remain unassigned. The map spans 3,740 cM with an average distance of 6.3 cM between markers. Fifty-five percent of the intervals are ≤5 cM and only 3% ≧20 cM. The present map demonstrates the cohesiveness of the different data sets and provides a single resource for genome scan analyses and integration with the radiation hybrid map.

We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.

Thoroughbred racehorses can damage several joints and bones due to rigorous training and racing, and develop various fractures during their athletic life. These fractures cause considerable wastage of racing Thoroughbreds. The fracture risk has been shown to be heritable in several species, although fractures in racehorses are generally believed to be influenced by various environmental factors such as speed and truck surface conditions. In this study, we estimated the heritability of the fracture risk in the Thoroughbred racehorse to clarify the genetic factors involved, by using Bayesian analysis with Gibbs sampling based on a categorized model. The clinical data of 3927 racehorses diagnosed by veterinarians of the Racehorse Clinics of Japan Racing Association were used. The health status regarding fractures was categorized as non-fracture, chip-fracture in the carpus, and other types of fractures. The heritability estimate (h2) for non-fracture versus fracture (all types of fractures), obtained from a nonlinear model, was 0.0911. Genetic factors were suggested to be involved in the fracture risk of Thoroughbred racehorses. The heritability estimate for chip-fracture in the carpus (h2 = 0.2598) was much higher than that for the other types of fractures (h2 = 0.0319). These results show that genetic factors relatively contribute to chip-fracture in the carpus, while environmental factors contribute to the other types of fractures. Based on the above results, we are conducting a genome-wide association study (GWAS) to identify candidate genes for chip-fracture in the carpus. At the presentation, we will also report the advances in the GWAS.

Indigenous horses in Japan, likely originating from the Mongolia-type horses, are distributed across the country and have formed some local populations: however, their population size has significantly decreased since the latter half of 19th century. Currently, their descendants remain only in eight local areas. Until date, autosome-based STR/SNP and matriline-based mitochondrial analyses to elucidate genetic relationship among the populations have been developed for preserving genetic resources and endemic characteristics. Recently, haplotype variation of equine Y chromosome has been identified for worldwide breeds. hi tins study, the distribution of Y haplotypes in the native populations was investigated to obtain their genetic information to further add to the results of previous studies. Blood DNA samples were obtained from 143 male/gelding horses of seven populations: 13 from Hokkaido: 37. Kiso; 38. Misaki: 7. Noma: 11. Taishu: 17. Miyako: and 20. Yonaguni. Haplotyping was performed by using five Y chromosomal loci. The SNP/indels of these loci were analyzed by direct sequencing of the targeted PCR amplicons. In these analyses. SNP variations were found at two loci. Y-45288 and -50869. The analyzed horse Y chromosomes were classified into three haplotypes. namely JHT-1. -2 and -3; these were identical to the previously reported haplotypes in worldwide breeds. The Hokkaido. Noma. Taishu and Miyako populations showed only JHT-1. On the other hand, both the Kiso and Misaki populations showed only JHT-2. Although JHT-1 and -3 were observed in the Yonaguni population. JHT-3 appeared due to a de novo mutation of JHT-1. Based on this result and previously repotted data of Asian horses, it can be assumed that JHT-1 is a major haplotype in ancestral native horses, which then became distributed and integrated into most of the modem horse populations. The fixation of JHT-2 also suggests influence by limited patrilines in the Kiso and Misaki populations. These findings complement the results of studies on the genetic features of Japanese native horse populations.

Microsatellites are useful tools for the construction of a linkage map and parentage testing of equines, but only a limited number of equine microsatellites have been elucidated. Thus, we constructed the equine genomic library enriched for DNA fragments containing (CAG) n repeats. The enriched method includes hybridization-capture of repeat regions using biotin-conjugated oligonucleotides, nucleotide substrate-biased polymerase reaction with the oligonucleotides and subsequent PCR amplification, because these procedures are useful for the cloning of less abundant trinucleotide microsatellites. Microsatellites containing (CAG) n repeats were obtained at the ratio of one per 3-4 clones, indicating an enrichment value about 10 4 -fold, resulting in less time consumption and less cost for cloning. In this study, 66 different microsatellites, (CAG) n repeats, were identified. The number of complete simple CAG repeats in our clones ranged 4-33, with an average repeat length of 8.8 units. The microsatellites were useful as sequence-tagged site (STS) markers. In addition, some clones containing (CAG) n repeats showed homology to human (CAG) n -containing genes, which have been previously mapped. These results indicate that the clones might be a useful tool for chromosome comparison between equines and humans. Key words: microsatellites, (CAG) n repeats, equine.