Genetic diversity and conservation in a small endangered horse population

Host Genetic Diversity and Infectious Diseases. Focus on Wild Boar, Red Deer and Tuberculosis

Host genetic diversity tends to limit disease spread in nature and buffers populations against epidemics. Genetic diversity in wildlife is expected to receive increasing attention in contexts related to disease transmission and human health. Ungulates such as wild boar (Sus scrofa) and red deer (Cervus elaphus) are important zoonotic hosts that can be precursors to disease emergence and spread in humans. Tuberculosis is a zoonotic disease with relevant consequences and can present high prevalence in wild boar and red deer populations. Here, we review studies on the genetic diversity of ungulates and determine to what extent these studies consider its importance on the spread of disease. This assessment also focused on wild boar, red deer, and tuberculosis. We found a disconnection between studies treating genetic diversity and those dealing with infectious diseases. Contrarily, genetic diversity studies in ungulates are mainly concerned with conservation. Despite the existing disconnection between studies on genetic diversity and studies on disease emergence and spread, the knowledge gathered in each discipline can be applied to the other. The bidirectional applications are illustrated in wild boar and red deer populations from Spain, where TB is an important threat for wildlife, livestock, and humans.

Major inconsistencies of inferred population genetic structure estimated in a large set of domestic horse breeds using microsatellites

STRUCTURE remains the most applied software aimed at recovering the true, but unknown, population structure from microsatellite or other genetic markers. About 30% of structure-based studies could not be reproduced (Molecular Ecology, 21, 2012, 4925). Here we use a large set of data from 2,323 horses from 93 domestic breeds plus the Przewalski horse, typed at 15 microsatellites, to evaluate how program settings impact the estimation of the optimal number of population clusters K opt that best describe the observed data. Domestic horses are suited as a test case as there is extensive background knowledge on the history of many breeds and extensive phylogenetic analyses. Different methods based on different genetic assumptions and statistical procedures (dapc, flock, PCoA, and structure with different run scenarios) all revealed general, broad-scale breed relationships that largely reflect known breed histories but diverged how they characterized small-scale patterns. structure failed to consistently identify K opt using the most widespread approach, the ΔK method, despite very large numbers of MCMC iterations (3,000,000) and replicates (100). The interpretation of breed structure over increasing numbers of K, without assuming a K opt, was consistent with known breed histories. The over-reliance on K opt should be replaced by a qualitative description of clustering over increasing K, which is scientifically more honest and has the advantage of being much faster and less computer intensive as lower numbers of MCMC iterations and repetitions suffice for stable results. Very large data sets are highly challenging for cluster analyses, especially when populations with complex genetic histories are investigated.

Inter- and intrabreed diversity of the major histocompatibility complex (MHC) in primitive and draft horse breeds

Background

Polymorphism of major histocompatibility complex (MHC) genes ensures effective immune responses against a wide array of pathogens. However, artificial selection, as performed in the case of domestic animals, may influence MHC diversity. Here, we investigate and compare the MHC diversity of three populations of horses, for which different breeding policies were applied, to evaluate the impact of artificial selection and the environment on MHC polymorphism.

Methods

Samples of DNA were taken from 100 Polish draft horses, 38 stabled Konik Polski horses and 32 semiferal Konik Polski horses. MHC alleles and haplotype diversity within and between these populations of horses was estimated from 11 MHC microsatellite loci.

Results

MHC diversity measured based on allelic richness, observed heterozygosity, expected heterozygosity and polymorphism content was similar across the MHC microsatellite loci in all three populations. The highest expected heterozygosity was detected in semiferal primitive horses (He = 0.74), while the lowest was calculated for draft horses (He = 0.65). In total, 203 haplotypes were determined (111 in Polish draft horses, 43 in semiferal Konik Polski horses and 49 in stabled Konik Polski horses), and four haplotypes were shared between the two populations of Koniks. None of these haplotypes were present in any of the previously investigated horse breeds. Intra-MHC recombination events were detected in all three populations. However, the population of semiferal Konik horses showed the highest recombination frequency among the three horse populations. In addition, three recombination events were detected.

Conclusions

These results showed that despite the different breeding policies, the MHC allele and haplotype diversity was similarly high in all three horse populations. Nevertheless, the proportion of new haplotypes in the offspring was the highest in semiferal Konik Polski horses, which indicates the influence of the environment on MHC diversity in horses. Thus, we speculate that the genetic makeup of the domestic horse MHC might be more strongly influenced by the environment than by artificial selection. Moreover, intra-MHC conversion, insertion, and deletion and intra-MHC recombination may be proposed as mechanisms underlying the generation of new MHC haplotypes in horses.

Animal and environmental factors associated with gestation length in the endangered Old Kladruber horse

Little is known about factors influencing gestation length in heavier types of horses. The objective was to assess the effects of the weight and age of mares, weight and sex of foals, lactation, month and year of conception, month of foaling, stallion and mare on gestation length in the endangered Old Kladruber breed that once served as a heavy coach horse for ceremonies of the Imperial Court in Vienna. The study was performed at the stud farm Slatinany, Czech Republic and reports data from foaling seasons between 2001 and 2018. A total of 649 gestations were included in the study. Gestation in mares weighing 680 kg and more was 1.9 days shorter than in those weighing up to 639 kg (P < 0.0001). Gestation in lactating mares was 3.9 days shorter than in non-lactating mares (P < 0.0001). Gestation was longest in mares conceiving in March (343.9 ± 0.60 days); thereafter it gradually shortened, with the shortest (P < 0.0001) in mares conceiving in July (334.9 ± 0.90 days). Gestation length in mares increased (P < 0.0001) from February foaling (340.4 ± 0.73 days) to March foaling (343.6 ± 0.55 days), and then decreased (P < 0.0001) up to the end of the breeding season in June (336.7 ± 0.92 days). Year of conception had an effect on GL (P < 0.02). Gestation in mares carrying male foals was 2.0 days longer than in those carrying female foals (P < 0.01). Gestation in mares delivering foals weighing 70 kg and more was 1.0 days longer than in those delivering foals weighing up to 60 kg (P < 0.01). Mare's age had no effect on gestation length. In conclusion, gestation length was associated with the weight of mares and foals, lactation, month and year of conception, month of foaling, and sex of foals.

Ocular abnormalities in a herd of Old Kladruber Horses: A cross-sectional study

OBJECTIVE

To screen a closed herd of the Old Kladruber Horses (OKH) for the prevalence of ocular disorders and report normal ocular variations.

ANIMALS STUDIED

Two hundred and sixty-one horses, 122 Old Kladruber Gray Horses, and 139 Old Kladruber Black Horses owned by the National Stud Farm Kladruby nad Labem, Czech Republic, were included in the study with signalment and pedigree information recorded.

PROCEDURES

Bilateral ocular examination of manually restrained horses was performed in a darkened environment by a single examiner (RA), using a portable slit-lamp biomicroscope, direct ophthalmoscope, and monocular indirect ophthalmoscopy using a Finnoff transilluminator and 20 D condensing lens. Fluorescein testing was performed when indicated.

RESULTS

The animal ages ranged from 3 months to 27 years (mean 7.82 years, median 6 years). The gender ratio (males:females) was 109:152. Ophthalmological abnormalities were found in 133 (50.96%) horses; with right and left eyes affected equally. The most common abnormalities were cataract formation (35 horses), iris hyperpigmentation (29 horses), alterations in corpora nigra size (26 horses), nonsenile vitreal degeneration (24 horses), linear keratopathy (11 horses), corneal stromal haze (nine horses) and corneal subepithelial punctate opacities (nine horses). The most frequent variations of normal ocular anatomy were posterior lenticular suture lines (222 horses), tapetal hypoplasia (95 horses) resulting in a multi-colored tapetal fundus (31 horses), nuclear sclerosis (48 horses), and senile vitreal degeneration (30 horses).

CONCLUSIONS

Ocular disorders were relatively common in OKH, but typically not vision threatening and not interfering with the quality of life.

Genetic monitoring of horses in the Czech Republic: A large-scale study with a focus on the Czech autochthonous breeds

We propose the first comprehensive in-depth study monitoring horses in the Czech Republic. We scanned 9,289 animals from 44 populations for 17 equine STRs. Other equids analysed involved Equus przewalskii and Equus asinus. The total of 228 different alleles were detected, with the mean number of 13.4 per locus. The highest allelic richness (AR) was found in the Welsh Part Bred (6.01), followed by the Camargue (5.93) and Czech Sport Pony (5.91), whereas the Friesian exhibited the lowest AR (3.06). Interpopulation differences explained approximately nine per cent of the total genetic diversity. Reynold's genetic distance ranged from 0.003 between the Czech Warmblood and the Slovak Warmblood to 0.404 between the Friesian and donkeys. Close genetic proximity between the Silesian Noriker and Noriker was revealed. The Moravian Warmblood was better differentiated and more distant from the Czech Warmblood than the Kinsky Horse and retained the original genes of the old Austro-Hungarian tribes. A high gene flow level and a lack of genetic structure were found in the seven studied populations. Despite the historical bottlenecks and previous inbreeding, the Czech-Moravian Belgian Horse, Hucul, Old Kladruber Horse and Silesian Noriker did not suffer a serious loss of genetic diversity due to genetic drift/low effective population size. A NeighborNet dendrogram revealed breeds not classified in their groups according to the nomenclature (the Friesian, Hafling and Merens).

Diversity and effective population size of four horse breeds from microsatellite DNA markers in South-Central Mexico

Abstract. The South-Central region of Mexico has experienced a sizeable introduction of purebred horses for recreational aims. A study was designed to assess effective population sizes and genetic diversity and to verify the genetic integrity of four horse breeds. Using a 12-microsatellite panel, Quarter Horse, Azteca, Thoroughbred and Creole (CRL) horses were sampled and analysed for diversity and genetic structure. Genetic diversity parameters showed high numbers of heterozygous horses but small effective population sizes in all breeds. Population structure results suggested some degree of admixture of CRL with the other reference breeds. The highly informative microsatellite panel allowed the verification of diversity in introduced horse populations and the confirmation of small effective population sizes, which suggests a risk for future breed integrity.

Development of novel associations between MHC alleles and susceptibility to parasitic infections in an isolated population of an endangered mammal

The role of pathogens in dynamics of endangered species is not fully understood, and the effect of infection often interacts with other processes affecting those species, such as fragmentation and isolation or loss of genetic variation. Small, isolated populations are prone to losing functional alleles due to demographic processes and genetic drift, which may diminish their ability to resist infection if immune genes are affected. Demographic processes may also alter the selective pressure exerted by a parasite, as they influence the rate of parasite transmission between individuals. In the present paper we studied changes in parasite infection levels and genetic variability in an isolated population of spotted suslik (Spermophillus suslicus). Over a three-year period (approx. three generations), when the population size remained relatively stable, we observed a considerable increase in parasite prevalence and infection intensity, followed by the development of novel associations between MHC DRB alleles and parasite burden. Contrary to expectations, the change in MHC allele frequency over time was not consistent with the effect of the allele - for instance, Spsu-DRB*07, associated with higher intensity of infection with a nematode Capillaria sp., increased in frequency from 11.8 to 20.2%. Yet, we found no signatures of selection in the studied loci. Our results show that an isolated, stable population may experience a sudden increase in parasitic infections, resulting in a development of novel associations between MHC alleles and parasite susceptibility/resistance, even though no signatures of selection can be found.