More than 400 million sheep are raised on the African continent, the majority of which are indigenous and are primarily reared for sustenance. They have effectively adapted to various climatic and ...production environments, surviving and flourishing. The genetic relationships among these sheep populations remain understudied. Herein, we sequenced the entire mitochondrial DNA control region of 120 animals from Hamary and Kabashi and their crossbreed (Hamary x Kabashi) of Sudan desert sheep (SDS) to understand their maternal-inherited genetic variation and demographic history profiles and relate those to the history of sheep pastoralism on the African continent. The results show a diversified and predominant D- loop haplogroup B (n = 102, 85%), with all other sequences belonging to haplogroup A. Most of the maternal genetic variation was partitioned between haplogroup (76.3%) while within haplogroup accounted for 23.7% of the variation. However, little genetic differentiation was observed among the two breeds and their crosses, with our results supporting a Hamari maternal origin for the crossbreed. Bayesian coalescent-based analysis reveals distinct demographic history between the two haplogroups, two breeds and their crosses. Comparison of the two haplogroup showed that haplogroup B experienced an earlier expansion than haplogroup A. Unlike the breed-based comparison, the expansion of the two breeds started roughly at the same time, around 6500 years ago, with Kabashi having a slightly greater effective population size. The maternal ancestors of SDS may have diverged before their introduction to the African continent. This study provides novel insights into the early history of these two main breeds of Sudan desert sheep and their crosses.
Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation ...and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a ~10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs-the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specific NEBL gene in a dachshund population and show that two of the NEBL candidate variants have regulatory potential in heart-derived cell lines and are associated with reduced NEBL isoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity.
In this study, influential factors and (co)variance components for survival to 24 h after birth were determined and estimated for Texel, Shropshire, and Oxford Down, the most common sheep breeds in ...Denmark. Data from 1992 to 2006 containing 138,813 survival records were extracted from the sheep recording database at the Danish Agricultural Advisory Service. Estimation of (co)variance components was carried out using univariate animal models, applying logistic link functions. The logistic functions were also used for estimation of fixed effects. Both direct and maternal additive genetic effects, as well as common litter effects, were included in the models. The mean survival to 24 h after birth was 92.5, 91.7, and 88.5% for Texel, Shropshire, and Oxford Down, respectively. There was a curvilinear relationship between survival to 24 h after birth and birth weight, with survival less for light and heavy lambs. Male lambs, as well as lambs from ewes in the first parity or with difficult lambing, had the least survival to 24 h after birth. Survival to 24 h after birth was greater in twin-born Texel and Shropshire lambs compared with singletons and vice versa in Oxford Down. Estimates of direct heritability were in the range from 0.05 to 0.07. Maternal heritability estimates were slightly greater (0.06 and 0.07) than direct heritabilities in Texel and Shropshire and less (0.04) in Oxford Down. The estimated genetic correlations between direct and maternal effects for survival to 24 h after birth were negative, which will make breeding for this trait more difficult. However, on the basis of estimated genetic parameters, it can be concluded that it is possible to improve survival to 24 h after birth in meat sheep breeds by accounting for both direct and maternal genetic effects in breeding programs.
Increased lamb production in the South-Eastern region of Kazakhstan confirms the economic feasibility of processing young sheep from 7 to 12 months. Unfortunately, domestic literature offers little ...information on the selection and appropriate use of 4-month-old lambs for this purpose; this accounts for the relevance and both scientific and practical significance of research aimed at increasing the meat productivity of 4-month-old lambs (depending on breed) in the semi-desert zone of the South-Eastern region of Kazakhstan, based on technological developments. The object of the study was lambs of fat-tailed coarse wool breeds: Edilbay, Hissar and Kazakh fat-tailed breeds. The animals were 4 months old and kept from birth in one flock at the Yntykbay farm in Almaty region. Among the three studied breeds, Gissar stands out in terms of carcass weight, slaughter weight, and specific gravity of the meat and carcass. High-quality carcasses were obtained from all groups; the Hissar breed had the yield of 17.5 kg (carcass yield was 78.3%).
The term high nature value (HNV) farming, acknowledges that the conservation of a large proportion of European biodiversity and important semi-natural habitats are dependent on low-input, mainly ...extensive farming practices. HNV has become a focus for nature conservation and countryside management in Europe. This paper critically analyses the drivers of change and the challenges facing two European HNV upland pastoralist systems, one in the French Atlantic Pyrenees and the other in the Irish uplands. The detailed case studies highlight the traditional linkages between the landscape, grazing management, locally adapted animal breeds and social capital, all of which are currently under threat from globalised markets and policy orientation. The research findings indicate that the European multifunctional model of agriculture and its support for farm diversification including the provision of environmental goods and services has not been successful in targeting and rewarding HNV systems. In the search for economic viability (and social acceptance) many are left with the stark choice of intensification or abandonment; ultimately meeting neither market demands nor ecosystem services. We conclude with a recommendation for more targeted, evidence based support for HNV farmland, along with better integration in the wider rural economy, if these farming practices are to survive into the future and if the EU is to meet its 2020 biodiversity targets.
•High nature value (HNV) farming systems have become a focus for nature conservation and countryside management.•High labour costs and low economic returns are forcing the simplification and specialisation of HNV pastoralist systems.•The European multiuse model of agriculture has not been successful in targeting and rewarding HNV farming systems.•We propose a clearer focus on farming systems in the delivery of ecosystem services.•HNV farming systems need to be more closely integrated within the wider rural economy.
•Diverse ancestry of the local Northern horse breeds revealed.•Genetic affinity found among geographically distant breeds.•Gene flow from transboundary breeds into an Estonian local breed confirmed.
...Sixteen microsatellite markers were used to assess the genetic diversity in native and imported transboundary horse breeds and populations from the Baltic Sea region, North-Eastern Europe and Asia (Mongolia and Yakutia, the Russian Federation), with a special focus on Estonian horse breeds. Testing for within-breed genetic variation, Hardy-Weinberg proportions, linkage disequilibrium between genotypes across loci, molecular variance, genetic relationships and population structure was performed.
The current microsatellite data indicated that the horse breeds in the Baltic Sea region, including all local Estonian, Finnhorse and Latvian horse breeds, have high within-breed variation. In terms of allelic richness and heterozygosity, the within-breed diversity was higher in the Estonian local breeds than in the Norwegian horse breeds.
On the basis of genetic distances, a distinguishable polarization amongst the breeds was observed in two breeds, the Arabian and the Døle, being the most distant and defining of the warm-blooded and the Norwegian breed groups, respectively. The local Estonian breeds, together with the Finnhorse, Mezen, Mongolian and Yakutian breeds, formed a sparse intermediate aggregate with a low variability, attributed to the differences among the breeds. The population structure analysis showed admixed ancestry in this small-size (pony type) breed group. Our study suggests that the local Nordic (Northern European) breeds (N = 11) formed three genetic clusters.
The introgression of genes from warm-blooded breeds was considerable in one of the Estonian local horse breeds, the Tori, as well as in the Latvian horse. Compared to the Tori and Latvian Horse, the Estonian Native, the Estonian Heavy Draught and the Finnhorse have preserved a unique gene pool to a larger extent and are more distinct.
Previous research has indicated that certain breeds of dogs stay longer in shelters than others. However, exactly how breed perception and identification influences potential adopters' decisions ...remains unclear. Current dog breed identification practices in animal shelters are often based upon information supplied by the relinquishing owner, or staff determination based on the dog's phenotype. However, discrepancies have been found between breed identification as typically assessed by welfare agencies and the outcome of DNA analysis. In Study 1, the perceived behavioral and adoptability characteristics of a pit-bull-type dog were compared with those of a Labrador Retriever and Border Collie. How the addition of a human handler influenced those perceptions was also assessed. In Study 2, lengths of stay and perceived attractiveness of dogs that were labeled as pit bull breeds were compared to dogs that were phenotypically similar but were labeled as another breed at an animal shelter. The latter dogs were called "lookalikes." In Study 3, we compared perceived attractiveness in video recordings of pit-bull-type dogs and lookalikes with and without breed labels. Lastly, data from an animal shelter that ceased applying breed labeling on kennels were analyzed, and lengths of stay and outcomes for all dog breeds, including pit bulls, before and after the change in labeling practice were compared. In total, these findings suggest that breed labeling influences potential adopters' perceptions and decision-making. Given the inherent complexity of breed assignment based on morphology coupled with negative breed perceptions, removing breed labels is a relatively low-cost strategy that will likely improve outcomes for dogs in animal shelters.
The Pecorans (higher ruminants) are believed to have rapidly speciated in the Mid-Eocene, resulting in five distinct extant families: Antilocapridae, Giraffidae, Moschidae, Cervidae, and Bovidae. Due ...to the rapid radiation, the Pecoran phylogeny has proven difficult to resolve, and 11 of the 15 possible rooted phylogenies describing ancestral relationships among the Antilocapridae, Giraffidae, Cervidae, and Bovidae have each been argued as representations of the true phylogeny. Here we demonstrate that a genome-wide single nucleotide polymorphism (SNP) genotyping platform designed for one species can be used to genotype ancient DNA from an extinct species and DNA from species diverged up to 29 million years ago and that the produced genotypes can be used to resolve the phylogeny for this rapidly radiated infraorder. We used a high-throughput assay with 54,693 SNP loci developed for Bos taurus taurus to rapidly genotype 678 individuals representing 61 Pecoran species. We produced a highly resolved phylogeny for this diverse group based upon 40,843 genome-wide SNP, which is five times as many informative characters as have previously been analyzed. We also establish a method to amplify and screen genomic information from extinct species, and place Bison priscus within the Bovidae. The quality of genotype calls and the placement of samples within a well-supported phylogeny may provide an important test for validating the fidelity and integrity of ancient samples. Finally, we constructed a phylogenomic network to accurately describe the relationships between 48 cattle breeds and facilitate inferences concerning the history of domestication and breed formation.
Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV ...differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its population genetics have been poorly explored in horses.
We investigated the patterns, population variation and gene annotation of CNV using the Axiom® Equine Genotyping Array (670,796 SNPs) from a large cohort of individuals (N = 1755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,640 SNP CNVs (individual markers), 18,800 segment CNVs (consecutive SNP CNVs of same gain/loss state or both) and 939 CNV regions (CNVRs; overlapping segment CNVs by at least 1 bp) compared to the average signal of the reference (Belgian draught horse) were identified. Our analyses showed that Equus caballus chromosome 12 (ECA12) was the most enriched in segment CNV gains and losses (~ 3% average proportion of the genome covered), but the highest number of segment CNVs were detected on ECA1 and ECA20 (regardless of size). The Friesian horses showed private SNP CNV gains (> 20% of the samples) on ECA1 and Exmoor ponies displayed private SNP CNV losses on ECA25 (> 20% of the samples). The Warmblood cluster showed private SNP CNV gains located in ECA9 and Draught cluster showed private SNP CNV losses located in ECA7. The length of the CNVRs ranged from 1 kb to 21.3 Mb. A total of 10,612 genes were annotated within the CNVRs. The PANTHER annotation of these genes showed significantly under- and overrepresented gene ontology biological terms related to cellular processes and immunity (Bonferroni P-value < 0.05). We identified 80 CNVRs overlapping with known QTL for fertility, coat colour, conformation and temperament. We also report 67 novel CNVRs.
This work revealed that CNV patterns, in the genome of some European horse breeds, occurred in specific genomic regions. The results provide support to the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.
Intervertebral disc (IVD) degeneration is common in dogs and can give rise to a number of diseases, such as IVD herniation, cervical spondylomyelopathy, and degenerative lumbosacral stenosis. ...Although there have been many reports and reviews on the clinical aspects of canine IVD disease, few reports have discussed and reviewed the process of IVD degeneration. In this first part of a two-part review, the anatomy, physiology, histopathology, and biochemical and biomechanical characteristics of the healthy and degenerated IVD are described. In Part 2, the aspects of IVD degeneration in chondrodystrophic and non-chondrodystrophic dog breeds are discussed in depth.
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