Genetic diversity of Cheju horses (Equus caballus) determined by using mitochondrial DNA D-loop polymorphism

We used sequence polymorphism of the mitochondrial DNA D-loop (968 bp excluding the tandem repeat region) to determine genetic diversity of horses inhabiting Cheju (a southern island of Korea). Seventeen haplotypes with frequencies from 1.5 to 21.5% were found among 65 Cheju horse samples. Genetic diversity (h) of the 17 haplotypes was calculated to be 0.91, indicating that the extant Cheju horse population consists of diverse genetic groups in their maternal lineage. Phylogenetic analysis showed that 17 types of Cheju (D-loop sequences determined), 5 Mongolian, 6 Arabian, 3 Belgian, 2 Tsushima, 2 Yunnan, 1 Przewalskii, and 3 Thoroughbred horses (published sequences for the latter seven breeds) showed that Cheju horses were distributed into many different clusters in the tree. Four Mongolian horses clustered with separate Cheju horse groups, showing that some Cheju horses are clearly of Mongolian origin. The analysis of partial sequences (284 bp) of the D-loop of 109 horses showed that Thoroughbred, Mongolian, Lipizzan, and Arabian breeds are as diverse as Cheju horses. Our data together with others' suggest that most horse breeds tested with reasonably sufficient numbers of samples are diverse in their maternal lineages and also are not uniquely different from each other.     

Genetic studies of blood markers in Przewalski's horses

Ninety-six Przewalski's horses (Equus przewalskii) were blood typed using systems of inherited blood variants known to be highly effective for parentage testing of domestic horses (E. caballus). Sixteen red cell antigenic factors detected using sera prepared by alloimmunization of domestic horses were shown to be inherited in six systems (A, C, D, P, Q, and U) and in the same patterns as domestic horses. Family data confirmed autosomal, codominant inheritance at five loci of serum protein variants (Al, Tf, Xk, Pi, and Es) and three loci of red cell proteins (PGM, PHI, and Hb). One serum protein locus (Gc) and two red cell protein loci (PGD and CA) appeared to be monomorphic. Despite the narrow genetic base and high inbreeding coefficients of captive Przewalski's horses, average heterozygosity calculated over 18 loci was estimated to be 0.320 +/- 0.05, which was similar to that found in five breeds of domestic horses.     

The study of cutaneous melanomas in Camargue-type gray-skinned horses (2): epidemiological survey

An epidemiological survey was made on cutaneous melanomas occurring in Camargue-type, gray-skinned horses in southern France. The population investigated was composed of 264 horses, which were selected from the Camargue horse stud registry and were allowed to be examined by the owners. The presence of tumors was inspected macroscopically according to the standardized protocols of veterinary medicine specialists, and some tumors were subjected to macroscopic histopathological examination. The results indicated that: 1) the prevalence of melanomas in the overall population was 31.4%; 2) the odds ratio was obtained for an age class of 5-9 years, in which most melanomas were presumed to occur; 3) the incidence of melanomas was significantly correlated with age, giving a prevalence of 67% at ages > 15 years; 4) the size and number of tumorous lesions were significantly related to age; 5) little correlation was observed between melanoma incidence and gender; and 6) the most frequently occurring body site of these tumors was underneath the tail. Because of their frequent occurrence in shaded body regions, sun exposure was not likely to be a risk factor for melanoma formation in these horses. In view of the slightly darker skin pigmentation in these horses at younger ages, the unique characteristics of their melanocytes may be associated with melanoma formation.     

A novel carbonic anhydrase from the mantle of the pearl oyster (Pinctada fucata)

A novel carbonic anhydrase (CA) has been purified from the mantle of the pearl oyster, Pinctada fucata, by ammonium sulfate precipitation and affinity chromatography. Its molecular mass was determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) to be approximately 38 kDa. Native-PAGE shows that the novel CA can bind a fluorescent probe, 5-dimethylamino-1-naphthalenesulfonamide (DNSA), known to specifically bind carbonic anhydrase. Compared to carbonic anhydrase I (CAI) from human erythrocytes, the novel CA migrates faster indicating that it is more acidic. The effect of an inhibitor on the enzyme activity was also examined. The CA from the mantle showed a weak resistance to acetazolamide (AZ), a specific inhibitor of CA. When DNSA was bound to CA, it caused the wavelength of emission maximum intensity to blue shift to 454 nm upon excitation at 326 nm. Histochemical data indicates that the enzyme is distributed widely throughout the mantle tissue, being concentrated at the edge of the mantle. The evidence presented indicates a function for CA in the process of pearl formation and biomineralization.     

Imputation of sequence level genotypes in the Franches-Montagnes horse breed

Background

A cost-effective strategy to increase the density of available markers within a population is to sequence a small proportion of the population and impute whole-genome sequence data for the remaining population. Increased densities of typed markers are advantageous for genome-wide association studies (GWAS) and genomic predictions.

Methods

We obtained genotypes for 54 602 SNPs (single nucleotide polymorphisms) in 1077 Franches-Montagnes (FM) horses and Illumina paired-end whole-genome sequencing data for 30 FM horses and 14 Warmblood horses. After variant calling, the sequence-derived SNP genotypes (~13 million SNPs) were used for genotype imputation with the software programs Beagle, Impute2 and FImpute.

Results

The mean imputation accuracy of FM horses using Impute2 was 92.0%. Imputation accuracy using Beagle and FImpute was 74.3% and 77.2%, respectively. In addition, for Impute2 we determined the imputation accuracy of all individual horses in the validation population, which ranged from 85.7% to 99.8%. The subsequent inclusion of Warmblood sequence data further increased the correlation between true and imputed genotypes for most horses, especially for horses with a high level of admixture. The final imputation accuracy of the horses ranged from 91.2% to 99.5%.

Conclusions

Using Impute2, the imputation accuracy was higher than 91% for all horses in the validation population, which indicates that direct imputation of 50k SNP-chip data to sequence level genotypes is feasible in the FM population. The individual imputation accuracy depended mainly on the applied software and the level of admixture.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0063-7) contains supplementary material, which is available to authorized users.     

The Study of Cutaneous Melanomas in Camargue‐Type Gray‐Skinned Horses (2): Epidemiological Survey

An epidemiological survey was made on cutaneous melanomas occurring in Camargue‐type, gray‐skinned horses in southern France. The population investigated was composed of 264 horses, which were selected from the Camargue horse stud registry and were allowed to be examined by the owners. The presence of tumors was inspected macroscopically according to the standardized protocols of veterinary medicine specialists, and some tumors were subjected to macroscopic histopathological examination. The results indicated that: 1) the prevalence of melanomas in the overall population was 31.4%; 2) the odds ratio was obtained for an age class of 5–9 years, in which most melanomas were presumed to occur; 3) the incidence of melanomas was significantly correlated with age, giving a prevalence of 67% at ages> 15 years; 4) the size and number of tumorous lesions were significantly related to age; 5) little correlation was observed between melanoma incidence and gender; and 6) the most frequently occurring body site of these tumors was underneath the tail. Because of their frequent occurrence in shaded body regions, sun exposure was not likely to be a risk factor for melanoma formation in these horses. In view of the slightly darker skin pigmentation in these horses at younger ages, the unique characteristics of their melanocytes may be associated with melanoma formation.     

The plasma protease inhibitor system (Pi) of Standardbred horses

The plasma protease inhibitor system (Pi) of Standardbred horses was studied by thin-layer, high-voltage, acid polyacrylamide gel electrophoresis (pH 4.6) followed by protein staining and staining for trypsin and chymotrypsin inhibition. In addition to the eight Thoroughbred alleles (PiF, G, I, L, N, S1, S2, U), another 10 alleles, designated PiH, J, K, O, P, Q, R, V, X, Z, were postulated to account for the 98 Pi types which were observed in Standardbreds. Detailed inhibitory spectra of the 'new' alleles were determined and further exceptions to the Pi1, Pi2 classification of Juneja et al. (1979) were found. Limited family data demonstrated the genetic nature of the 'new' variants and confirmed the allelic inheritance of the 'new' Pi variants.     

Genetic polymorphism of horse serum protein 3 (SP3)

Two-dimensional agarose gel (pH 8.6)-horizontal polyacrylamide gel (pH 9.0) electrophoresis of horse serum samples, followed by general protein staining, revealed genetic polymorphism of an unidentified protein tentatively designated serum protein 3 (SP3). The SP3 fractions appeared distinctly when a 14% concentration of acrylamide was used in the separation gels. The 2-D mobilities of SP3 fractions were quite similar to that of albumin. Family data were consistent with the hypothesis that the observed SP3 phenotypes were controlled by four co-dominant, autosomal alleles (D, F, I, S). Evidence was provided that the F allele can be further divided into two alleles (F1 and F2); the mobilities of F1 and F2 variants were very similar. Each of the SP3 alleles gave rise to one fraction and each of the heterozygous types showed two fractions. More than 600 horses representing five different breeds (Swedish Trotter, North-Swedish Trotter, Thoroughbred, Arab and Polish Tarpan) were typed for SP3, and allele frequency estimates were calculated. SP3 was highly polymorphic in all breeds studied.     

Genetic variability and population differentiation in captive baird's Tapirs (Tapirus bairdii)

The objectives of this study were to assess the level of genetic variability and population differentiation within captive populations of an endangered large mammal, Baird's tapir (Tapirus bairdii). We genotyped 37 captive animals from North American (NA) and Central American (CA) zoos and conservation ranches using six polymorphic microsatellite loci. Standard indices of genetic variability (allelic richness and diversity, and heterozygosity) were estimated and compared between captive populations, and between captive and wild population samples. In addition, we evaluated levels of population differentiation using Weir and Cockerham's version of Wright's F-statistics. The results indicate that the NA and CA captive populations of Baird's tapirs have retained levels of genetic variability similar to that measured in a wild population. However, inbreeding coefficients estimated from the molecular data indicate that the CA captive population is at increased risk of losing genetic variability due to inbreeding. Despite this, estimated levels of population differentiation indicate limited divergence of the CA captive population from the wild population. Careful management appears to have kept inbreeding coefficients low in the NA captive population; however, population differentiation levels indicate that the NA population has experienced increased divergence from wild populations due to a founder effect and isolation. Based on these results, we conclude that intermittent exchanges of Baird's tapirs between the NA and CA captive populations will benefit both populations by increasing genetic variability and effective population size, while reducing inbreeding and divergence from wild populations. Zoo Biol 23:521–531, 2004. © 2004 Wiley-Liss, Inc.     

An Outbreak of Type A(2) Influenza Among Horses

The clinical diagnosis of equine influenza was first based on the spectacular contagiousness of the disease, the general clinical resemblances to human influenza and the almost complete absence of complications usually observed in infectious viral arteritis, viral rhinopneumonitis or in other respiratory infections of the horses. The specific viral etiology of the epizootic was ascertained through the isolation of a type A influenza virus and further substantiated by evaluation of the immunological response of the sick horses, as demonstrated by complement fixation and hemagglutination-inhibition tests, using normal and convalescent sera. The agent isolated was typed and proved to be similar to a type A(2) virus isolated from humans this year. Because of the widespread nature of this epizootic, one cannot exclude the possibility that was an expression of an attack by the virus on an unprotected population of horses without previous infectious experience with the influenza virus. Even though mortality and serious complications or sequelae were negligible in this present outbreak, heavy financial losses were suffered by owners, track operators and others. Future epizootics may well be of an even more severe nature. Attention must be focused on the control of this disease, not only on account of its veterinary and economic aspects but also because of the possibility that horses might be a reservoir of infection for humans.     

Purification and some kinetic properties of carbonic anhydrase from rainbow trout (Oncorhynchus mykiss) liver and metal inhibition

In the present study, carbonic anhydrase (CA) enzyme was purified from rainbow trout (RT) liver with a specific activity of 4318 EUxmg(-1) and a yield of 38% using Sepharose-4B-L tyrosine-sulfanilamide affinity gel chromatography. The overall purification was approximately 2260-fold. To check the purity and determine subunit molecular weight of enzyme, SDS-polyacrylamide gel electrophoresis was performed, which showed a single band and MW of approx. 29.4 kDa. The molecular weight of native enzyme was estimated to be approx. 31 kDa by Sephadex-G 200 gel filtration chromatography. Optimum and stable pH were determined as 9.0 in 1 M Tris-SO(4) buffer and 8.5 in 1 M Tris-SO(4) buffer at 4 degrees C, respectively. The optimum temperature, activation energy (E(a)), activation enthalpy ((DeltaH) and Q(10) from Arrhenius plot for the RT liver CA were 40 degrees C, 2.88 kcal/mol, 2.288 kcal/mol and 1.53, respectively. The purified enzyme had an apparent K(m) and V(max) of 0.66 mM and 0.126 micromol x min(-1) for 4-nitrophenylacetate, respectively. K(cat) of the CA was found to be 32.8 s(-1). The inhibitory effects of low concentrations of different metals (Co(II), Cu(II), Zn(II) and Ag(I)) on CA activity were determined using the esterase method under in vitro conditions. The obtained IC(50) values, 50% inhibition of in vitro enzyme activity, were 0.03 mM for cobalt, 30 mM for copper, 47.1 mM for zinc and 0.01 mM for silver. K(i) values for these substances were also calculated from Linewaever-Burk plots as 0.050 mM for cobalt, 1.950 mM for copper, 7.035 mM for zinc and 2.190 mM for silver respectively and determined that cobalt and zinc inhibit the enzyme a competitive manner and copper and silver inhibit the enzyme in an uncompetitive manner.     

Genetic polymorphism of horse serum protein 3 (SP3)

Summary. Two-dimensional agarose gel (pH 8.6)-horizontal polyacrylamide gel (pH 9.0) electrophoresis of horse serum samples, followed by general protein staining, revealed genetic polymorphism of an unidentified protein tentatively designated serum protein 3 (SP3). The SP3 fractions appeared distinctly when a 14% concentration of acrylamide was used in the separation gels. The 2-D mobilities of SP3 fractions were quite similar to that of albumin. Family data were consistent with the hypothesis that the observed SP3 phenotypes were controlled by four co-dominant, autosomal alleles ( D,F,I,S ). Evidence was provided that the F allele can be further divided into two alleles ( F ₁ and F ₂); the mobilities of F₁ and F₂ variants were very similar. Each of the SP3 alleles gave rise to one fraction and each of the heterozygous types showed two fractions. More than 600 horses representing five different breeds (Swedish Trotter, North-Swedish Trotter, Thoroughbred, Arab and Polish Tarpan) were typed for SP3, and allele frequency estimates were calculated. SP3 was highly polymorphic in all breeds studied.     

Multiple genotypes of mitochondrial DNA within a horse population from a small region in Yunnan province of China

mtDNA genotypes of six domestic horses (three adult short horses whose heights are under 1 m and three common domestic horses) from a small region of 15 km² in Malipo county of Yunnan province of China were investigated by the technique of restriction fragment length polymorphism (RFLP) with 16 restriction endonucleases which recognize 6-bp sequences. An average of 56 fragments for an individual was obtained. Unlike other domestic animals, this population of horses exhibits high mtDNA genetic diversity. Each of the six horses has a specific mtDNA genotype showing a pattern of multiple maternal origins, as suggested by fossil and literature records. We think the population of horses is an amazing seed-resource pool of horses and hence deserves to be paid more attention from the view of conservation genetics. However, it is also remarkable that we did not find any typical mtDNA genetic markers which would discriminate between short horses and common domestic horses.     

Facial hair whorls (trichoglyphs) and the incidence of motor laterality in the horse

Several species demonstrate obvious motor laterality (sidedness, handedness) in their motor function. Motor laterality in the horse affects locomotion and subsequently equine performance during training and may have inherent safety implications for equitation. Some of the most commonly used identification features in the horse are hair whorls (trichoglyphs), since their specific location and character vary to some degree in every horse. We investigated the relationship between the hair flow of single facial hair whorls and the incidence of lateralised motor bias in 219 horses when under saddle in ridden work. The horses exhibited significant differences in motor preferences with 104 left-lateralised (LL) horses, 95 right-lateralised (RL) horses compared to only 20 well-balanced (WB) horses (chi(2)=36.9, d.f.=2, P<0.01). There was also a significant difference in the frequency distribution of single facial hair whorl patterns in the horses consisting of 114 horses with counter-clockwise (CC) whorls, 82 horses with clockwise (C) whorls and 23 horses, which had radial (R) whorls (chi(2)=38.87, d.f.=2, P<0.01). Overall there was a statistically significant association between motor behaviour and facial hair whorl patterns in the horses (chi(2)=69.4, d.f.=4, P>0.001). The RL horses had significantly more C facial hair whorls and the LL horses had significantly more CC facial hair whorls than would be expected purely by chance alone (P<0.05). The findings may provide trainers with a useful tool when attempting to identify simple, non-invasive and reliable predictors of motor laterality in the horse. Furthermore, given that efficient targeted training of performance horses during ridden work may produce WB equine athletes, the findings could assist trainers when designing individual-specific training programmes for young horses.     

A Cultural History of Animals (6 Volumes)

ABSTRACT

Handling and training methods of horses, which specially emphasize the importance of understanding horse body language and the use of reinforcements, are often used in practice, yet their effects are not completely known. This study investigated whether the use of a sympathetic approach during the preparation for public auctions influenced the reactivity of young horses towards humans. Sixteen thoroughbred yearlings were prepared for the public auctions during one month: eight horses (“Control”) were handled according to conventional practices, while the others (“Treated”) were handled with two sessions of basic training based on body language. The reactivity of horses was assessed in the presence of an “unfamiliar person” and a “familiar person” inside the horse's box. The experimenter recorded the presence/absence of selected behaviors during seven observational moments: “approaching the box,” “opening the box door,” “entering the box,” and four consecutive observations every thirty seconds. Reactivity of horses was ranked during the first experience of “bit,” “grooming,” “shower,” and application of the “surcingle.” Heart rate was telemetrically recorded during this final test. At the end of the auction preparation, “Treated” horses exhibited more “contact” (p = 0.08) and “lick” (p < 0.05) behaviors in the presence of a person. “Control” horses showed higher (non-significant) percentages of negative (more nervous) rankings during “bit,” “grooming,” and “surcingle” tests. Two “Control” horses showed aggressive behavior during the application of the surcingle and the test was interrupted to guarantee person and animal safety. In this pilot study, horses handled with a sympathetic approach showed less reactive behaviors compared with “Control” horses. It would be interesting to enlarge the sample size and assess if the use of non-coercive handling during the whole training period influences their welfare positively and for a long time.     

The plasma protease inhibitor system (Pi) of Standardbred horses

The plasma protease inhibitor system (Pi) of Standardbred horses was studied by thin-layer, high-voltage, acid polyacrylamide gel electrophoresis (pH 4.6) followed by protein staining and staining for trypsin and chymotrypsin inhibition. In addition to the eight Thoroughbred alleles ( Pi^{F, g, i, L, N, S1, S2, u)} , another 10 alleles, designated PiH, j, k, ^o, ^p, ^q , ^r, ^v, ^{x, z}, were postulated to account for the 98 Pi types which were observed in Standardbreds. Detailed inhibitory spectra of the 'new' alleles were determined and further exceptions to the Pil, Pi2 classification of Juneja et al. (1979) were found. Limited family data demonstrated the genetic nature of the 'new' variants and confirmed the allelic inheritance of the 'new' Pi variants.     

Multiple pathways in diaspore dispersal, exemplified by studies of Noogoora Burr (Xanthium occidentale Bertol., Compositae)

LIDDLE, M. J. & ELGAR, M. A., 1984. Multiple pathways in diaspore dispersal, exemplified by studies of Noogoora Burr ( Xanthium occidmtale Bertol., Compositae). Some of the ways in which the burrs are dispersed and some of the factors that may cause changes between the different dispersal pathways were examined. Populations of burrs were marked on the plants in an ungrazed paddock, a paddock grazed by horses, and a paddock grazed by sheep. Eleven percent of the marked populations were recovered from the hair of horses and 26% from the sheeps' wool. A single flood removed 80% of one population. Burrs moved a mean distance of 30 cm on paths used by horses and 18% were buried in the path soil. Burrs were placed in animals' hair by hand. After 16 days, sheep retained 76% of the burrs in their wool, while only 2% remained in the hair of horses and cattle. An experiment showed that burrs may be catapulted up to a distance of 3.3 m from the plants.
A model is presented which outlines the alternative or sequential pathways that may be followed by the burrs. Occasional events, such as flooding and presence or absence of stock, were the main causes of changes between pathways. In the model, these dispersal mechanisms are considered as release-phase and substrate-phase processes. Each process derives its energy from different sources and may be modified by inputs of energy from other sources.     

Estimation of the fertility rates of Japanese wild boars (Sus scrofa leucomystax) using fetuses and corpora albicans

Effective population control of Japanese wild boar (Sus scrofa leucomystax) requires reliable information about population dynamics. Fertility rate is the fundamental component of reproduction to evaluate population dynamics. However, little is known regarding the fertility rate of Japanese wild boar. The traditional hunting practices make it difficult to obtain pregnant females and calculate the fertility rate by checking fetuses as is performed in other countries. Therefore, we focused on the corpora albicans (CA) as the CA remains in the ovaries of postpartum females after pregnancy. This study aimed to evaluate the utility of CA and estimate the fertility rate of Japanese wild boars using CA. Histological analysis of ovaries enabled us to discriminate type 1 CA, which remains for 1 year after breeding. Type 1 CA is a superior indicator compared with lactation in the non-pregnancy season because it allows verification of postpartum females over a long period. The fertility rate was calculated by the combination of pregnant and postpartum females using fetuses and type 1 CA from April to November. The fertility rate of the females captured after the second pregnancy season was 90.3 % during the pregnancy period and 100 % during the non-pregnancy period. The high fertility rate of adult females suggests that intensive adult female harvesting is needed. Our new method to determine fertility rates contributes to developing a monitoring system to adequately control Japanese wild boar population.     

Carbonic anhydrase isozymes in American ponies and riding horses: A new polymorphic high-activity type isozyme

A study of the erythrocyte carbonic anhydrases of 219 American ponies and 76 riding horses has revealed the presence of five variants of the low-activity CA B isozyme and two variants of the high-activity CA C isozyme. The previously undetected variant of CA C was found only in the pony population and had an allele frequency of 8.9%. A family study of animals possessing the CA B variant A ₂ showed an unexpected high frequency of inheritance.     

Population Genetic Structure and Differentiaton of Parashorea chinensis(Dipterocarpaceae)

The genetic diversity and population differentiation of Parashorea chinensis, a rare and endangered dipterocarp, and listed in the Plant Red Book under Grade I, were examined using allozyme analysis of horizontal sliceable starch gel electrophoresis. Considering its narrow distribution, which was limited in the South & Southeast of Yunnan and Southwest of Guangxi, allozyme data for 16 loci of 11 enzymes in 9 natural population (as a comparison, two cultivated populations in Xishuangbanna Tropical Botanical Garden were analyzed) indicated extremely low level of genetic variability in these eleven populations with the proportion of polymorphic loci(P) ranging from 6.25% to 12.5%(mean 6.82%).