Sheep Breeds Research Articles

Analysis of genotyping data reveals the unique genetic diversity represented by the breeds of sheep native to the United Kingdom

BackgroundSheep breeds native to the United Kingdom exhibit a striking diversity of different traits. Some of these traits are highly sustainable, such as seasonal wool shedding in the Wiltshire Horn, and are likely to become more important as pressures on sheep production increase in coming decades. Despite their clear importance to the future of sheep farming, the genetic diversity of native UK sheep breeds is poorly characterised. This increases the risk of losing the ability to select for breed-specific traits from native breeds that might be important to the UK sheep sector in the future. Here, we use 50 K genotyping to perform preliminary analysis of breed relationships and genetic diversity within native UK sheep breeds, as a first step towards a comprehensive characterisation. This study generates novel data for thirteen native UK breeds, including six on the UK Breeds at Risk (BAR) list, and utilises existing data from the publicly available Sheep HapMap dataset to investigate population structure, heterozygosity and admixture.ResultsIn this study the commercial breeds exhibited high levels of admixture, weaker population structure and had higher heterozygosity compared to the other native breeds, which generally tend to be more distinct, less admixed, and have lower genetic diversity and higher kinship coefficients. Some breeds including the Wiltshire Horn, Lincoln Longwool and Ryeland showed very little admixture at all, indicating a high level of breed integrity but potentially low genetic diversity. Population structure and admixture were strongly influenced by sample size and sample provenance – highlighting the need for equal sample sizes, sufficient numbers of individuals per breed, and sampling across multiple flocks. The genetic profiles both within and between breeds were highly complex for UK sheep, reflecting the complexity in the demographic history of these breeds.ConclusionOur results highlight the utility of genotyping data for investigating breed diversity and genetic structure. They also suggest that routine generation of genotyping data would be very useful in informing conservation strategies for rare and declining breeds with small population sizes. We conclude that generating genetic resources for the sheep breeds that are native to the UK will help preserve the considerable genetic diversity represented by these breeds, and safe-guard this diversity as a valuable resource for the UK sheep sector to utilise in the face of future challenges.

Spatial distribution of available phosphorus in surface road and trackway surface materials on a sheep farm in Ireland

Farm roadway runoff is a high-risk source of pollution when connectivity with waters occurs. Nutrients in this runoff are dominated by fresh animal deposits, but recent dairy and beef farm studies showed that available phosphorus (P) accumulates in roadway surface material and can be lost in runoff. A current knowledge gap is to examine available P concentrations in unsealed roadway and trackway (non-maintained) network of a lowland sheep farm. The present study focused on a 45 ha farm stocked with 544 sheep in south-east Ireland. Ten locations were sampled along with the adjacent fields for available P (i.e., Morgan’s P) and ancillary parameters (e.g., pH, total P and heavy metals) in December 2022. The first sampling location was on an aggregate roadway and the other nine were on trackways representing an older aggregate roadway network used by the flock but now covered with soil and grass. Results showed a distinct difference in surface material pH between roadway and trackway locations. Trackways had a pH that mimicked adjacent fields around the agronomic optimum for grassland of ∼6.2. All sampling locations had elevated available P concentrations, ranging from 26.3 to 111.0 mg L−1 (mean 62.8 mg L−1), similar to the spatial distribution for dairy farms but above those found at beef farms previously studied. The highest available P concentrations were found in roadway and trackway sections adjacent to the farmyard. Other elevated sampling areas were on trackways (87.3 or 97.7 mg P L−1) away from the farmyard where sheep are funnelled to pasture, stop to seek shade, urinate and defecate but do not graze. By contrast the average available P concentration for the surrounding fields was 8.4 mg L−1 with a range of 2.7–15.9 mg L−1. Two sampling areas combine to create a critical source area where a high available P source becomes visibly mobilised as runoff during rainfall, discharges into an open drainage ditch, which is then connected to a local stream. Breaking the pathway before runoff enters the open ditch could be a cheap and effective way of mitigating nutrient losses at these two locations.

Comparative Analysis of the Distribution of the Main Helminthiasis Causative Agents in the Absheron Peninsula and Khizi Region

The research was conducted on sheep farms located in the Absheron region in 2015-2020. The major helminth fauna in sheep in the private and farmer farms of the Absheron region was found to consist of helminth species: Fasciola hepatica, F. gigantica, Dicrocoelium lanceatum, Paramphistomum cervi, Moniezia expansa, M. benedeni, Taenia hydatigena, T. ovis, Multiceps multiceps, Echinococcus granulosus, Protostrongylus hobmaieri, P. kochi, P. railleti, Muellerius capillaris, Trichocephalus ovis, Chabertia ovina, Haemonchus contortus, Dictyocaulus filaria. The extensiveness and intensity of the distribution of the 18 main helminths detected in the region by the complete helminthological dissection method in 19 research areas (14 in the Absheron peninsula: Zire, Hovsan, Mashtagha, Mehdiabad, Gobu, Sulutepe, Z. Taghiyev, Fatmayi, Novkhani, Mammadli, Khirdalan, Jeyranbatan, Mushvigabad, Guzdek; 5 in the Khizi region: Yeni Yashma, Shorabad, Altiaghaj, Gizilgazma, Tudar) are described in tables. Higher invasion levels were identifi­ed for T. ovis(43.2%, 1-53 samples), E. granulosus (39.2%, 1-18 samples), H. contortus (35.0%, 2-56 samp­les), and they we­re con­si­de­red the do­mi­nant hel­minth spe­ci­es of the re­gi­on. Ba­sed on the complete helminthological dissection, in the Absheron peninsula, IE was 17.7% and II was 1-64 samples, and in the Khizi district, IE was 29.0% and II was 1-83 samples. Thus, complete helminthological examination methods allowed us to conclude that the infection rate in the Khizi region is higher than in the Absheron Peninsula. This makes it necessary for farmers and veterinarians to start veterinary sanitary measures, both prophylactic and treatment measures against helminths in the Khizi district.

Caracterización sociocultural y económica de producción de ovinos en comunidades indígenas, Tungurahua - Ecuador

Sheep production in Ecuador is mostly for self-consumption in rural areas and especially in indigenous communities, although some marketing practices may eventually be implemented with products derived from sheep farming, such as milk and wool, which, in addition come into play in the processes of sustaining cultural traditions. Starting from this conviction, this article aims to describe the sociocultural and economic characteristics of sheep production in the indigenous communities of the province of Tungurahua, among which the communities stand out, within the study area: Quisapincha, Tomabela, Chibuleos and the Salasacas. The methodology that guides the research is qualitative, with a documentary and field design, since it is, on the one hand, exposing some sociocultural features of the study population, as well as specifying economic variables of sheep production in the region. . The theoretical review shows the importance of sheep farming as a source of income for a good number of people from the indigenous communities in the country, also representing a factor of preservation of the native cultures settled in regions such as the Tungurahua Province. Among the conclusions derived from empirical observation, it can be added that in the indigenous sectors of the province, there is evidence of a lack of knowledge of the basic health systems that must be implemented on their farms, which affects production and the economic strength of production.

PSXII-19 Influence of dietary copper concentration and liver sampling location on liver copper concentrations in three breeds (Gulf Coast Native, Suffolk x Hampshire, and Jacob) of sheep

Abstract Male sheep (n = 27) from three different breeds: 1) Gulf Coast Native (GCN; n = 9 wethers), 2) Suffolk x Hampshire (SHC; n = 9 wethers), and 3) Jacob (JCB; n = 9 intact males) approximately 9 mo of age, [body weight (BW) = 38.16 ± 2.43 kg) were stratified by BW and breed into 3 treatment groups to examine the impact of breed, supplemental copper (Cu) dose, and liver sampling location on liver Cu concentrations. On d 0 of the experiment, liver biopsies were collected from 5 sheep per breed and analyzed for Cu concentrations. Animals were housed in individual pens and received 2% of BW of a pelleted concentrate containing the appropriate Cu treatment once daily and hay in amounts to allow ad libitum access to hay over a 24 h period. Treatments consisted of 1) low Cu (LCu; 15.3 mg Cu/kg DM), 2) moderate Cu (MCu; 17.7 mg Cu/kg DM), and 3) high Cu (HCu; 23.8 mg Cu/kg DM) from CuSO4∙5H2O. On d 50 of the experiment, all animals were weighed and transported to an USDA inspected abattoir and harvested. Following harvest, samples were obtained from the left and right lobes of the liver and thoroughly washed with phosphate-buffered saline. All liver samples were dried, ashed, and reconstituted in 5 mL of 1.2 N HCl for Cu analysis. Data were analyzed as a randomized block design using the MIXED procedure in SAS with individual animal as the experimental unit. There was a three-way interaction between breed x treatment x liver lobe (P < 0.04). The right liver lobe in HCu JCB sheep had greater (P < 0.05) Cu concentrations compared with the left liver lobe. Both the left and right lobes of the liver had greater (P < 0.001) Cu concentrations compared with the initial liver Cu concentration in MCu JCB sheep. The right liver lobe of HCu GCN sheep tended (P < 0.07) to have greater liver Cu concentrations compared with the left liver lobe. The Cu concentration in the right liver lobe tended (P < 0.09) to be greater in MCu sheep compared with the left liver lobe. Liver Cu concentrations within the right lobe of HCu GCN sheep were greater (P < 0.05) than liver Cu concentrations in the right and left liver lobe samples in LCu GCN sheep. Liver Cu concentrations in SHC sheep were not influenced by treatment. Future research examining the impact of breed and Cu supplementation on the molecular mechanisms associated with Cu absorption, storage, and excretion is warranted.

PSIV-16 The role of veterinary services on nutrition schemes, management, and health practices for sheep and goats in rural Ngaka Modiri Molema District Municipality, North West Province of South Africa

Abstract Poverty is a feature of rural households, and as a result rural people usually adopt low-input agriculture to alleviate poverty. Many households in Ngaka Modiri Molema District keep animals, particularly sheep and goats, for a variety of reasons, including as source of income, milk, and meat. However, they lack the management skills that are necessary for their livestock to increase their productivity. Inadequate animal management, including poor feeding and housing standards and poor application of proper animal health procedures are compounded by a lack of agricultural experience and low-input farming methods. In addition, poor animal nutrition, sickness and a high prevalence of parasites, and low animal production output further contribute to low overall productivity. Therefore, support offered by the veterinary services, and the impact these interventions have on sheep and goat farming among rural farmers need to be investigated. The present study will seek to describe the feeding schemes and management practices adopted by sheep and goat owners, as well as the role of veterinary and extension services in the development of such practices. Health care provided to sheep and goat farmers by the veterinary services will also be determined. A survey will be conducted in Ngaka Modiri Molema District Municipality, a rural area in North West Province of South Africa. The study population will consist of all farmers, both female and male, rearing sheep and goats. Animal and farm information level data and general farm management practices will be collected via a questionnaire survey. Using the Statistical Kit for STATA (version 16), data will be examined by computing frequency, percentages, and proportions based on the characteristics of the sample population. This survey will help to provide opportunities for resource-poor farmers in rural areas to develop their flocks.

PSIV-14 Short-term heat stress affects the plasma metabolome of Florida Cracker sheep

Abstract Florida Cracker sheep is a heritage sheep breed and an endangered species that was developed under natural selection in Florida, US. The objective of this study was to evaluate the effect of short-term heat stress on the plasma metabolome of Florida Cracker ewes (2 yr). A total of fourteen ewes were allocated to heat stress (HT, n = 7) or cooling (CTL, n = 7) conditions for 6 wk during the summer season. Treatment groups were grouped in covered concrete floor pens with similar dimensions and characteristics and had access to shelter, feed, and freshwater ad libitum. The HT pen was exposed to regular ambient temperatures, and for the cooling pen, an evaporative cooling fan was used. Data for ambient temperature and relative humidity of HT and CTL pens were recorded every week to estimate the temperature humidity index (THI). Blood samples were collected from each experimental ewe 1 wk before the start of the experiment (baseline) and at wk 1, 2, 3, 4, 5, and 6 post-treatment. Plasma was extracted from the blood and processed for targeted metabolomics. Targeted metabolomics was performed using Nuclear Magnetic Resonance spectroscopy to quantify a total of 50 metabolites, including organic acids, amino acids, hexoses, lipids, and carnitines. Statistical analysis for biomarker and pathway enrichment was performed using Metaboanalyst 5.0. The THI values for the HT and THI groups ranged from 81.3 to 89.5 and from 73.5 to 75.6, respectively. A total of 19 differentially abundant metabolites were identified between HT and CTL. The pathway enrichment analysis showed upregulation of fatty acid and primary bile biosynthesis, and glutathione, porphyrin, glycine, serine, and threonine metabolism (P ≤ 0.05) in HT compared with CTL sheep. These metabolic pathways could have a role in the response of the ewes to short-term HT. Our findings highlight that short-term HT alters the plasma metabolome of Florida Cracker ewes. Understanding these changes can contribute to the development of effective management strategies to mitigate the detrimental impact of HT on sheep operations in the Southern US.

503 Selection signatures in a prolific meat sheep breed

Abstract In sheep meat production, prolificity is one of the main factors influencing economic profitability of a farm. Belclare sheep are used for meat production and have passed through intense selection pressure to high prolificity, leading them to have large litter sizes. This study aimed to identify selection signature regions and carry out functional analyses related to reproduction traits in the Belclare breed in contrast to a group of non-prolific meat breeds. A total of 50,166 biallelic SNPs from the Illumina OvineSNP50 genotyped in the Belclare breed (n = 2,377) and four meat breeds (Beltex, n = 146; Charollais, n = 1,477; Suffolk, n = 1,231 and Texel, n = 3,330). SNP filtering and quality control were performed within each breed using PLINK v1.9. Only SNPs on autosomal chromosomes with defined positions according to the sheep (Ovis aries) genome assembly OAR3.1 were analyzed. Samples and SNPs with a call rate below 95% were discarded, as well as SNPs with MAF below 1% and deviation of Hardy-Weinberg equilibrium with P-value ≤ 10-6. Imputation of missing genotypes and haplotype phasing were performed using BEAGLE v.3.3.2. After quality control, an average of 30,249 SNPs were further analyzed. Selection signature detection was performed by Cross-Population Extended Haplotype Homozygosity (XP-EHH) and Ratio of Site-specific Extended Haplotype Homozygosity between populations (Rsb), with the REHH v.3.2.2 software in R, using 100 kb non-overlapping windows with at least two markers per window. The top 1% windows with the greatest average values were considered regions under positive selection. Gene and QTL annotation were conducted with the GALLO R package. Gene and metabolic pathways enrichment (FDR< 0.10) were performed with gprofiler2 software. A total of 67 genomic regions co-localized with 76 candidate genes and 65 QTLs were identified. The genes were enriched for 12 molecular function terms. Among the annotated genes, FSHR, INSL6, HSD17B12, and SGK1 were previously found to be related to reproduction traits. The enriched term follicle-stimulating hormone receptor activity was related to the FSHR gene. The follicle-stimulating hormone (FSH) has an important role in follicular development, and their concentrations are regulated by the FSH receptor (FSHR), which suggests that FSHR is also involved in prolificity of the ewe. The testes weight trait was detected in the reproductive QTL class, but no gene related to fertility was identified. The gene INSL6 is associated with spermatogenesis and sperm motility and, as Belclare rams are used to produce prolific replacements, it may have an important role in semen quality and prolificity, as increased semen quality might increase the chance of a successful fecundation. The identification of selection signatures highlights that the selection pressure left footprints in the Belclare breed genome related to reproduction, which may affect the litter sizes.

Succession of rumen microbiota and metabolites across different reproductive periods in different sheep breeds and their impact on the growth and development of offspring lambs

BackgroundThe microbiota and metabolites in the gastrointestinal tracts of female animals at different reproductive periods are very important to the growth, development, and health of themselves and their offspring. However, the changes in the gastrointestinal microbiota and metabolites throughout reproductive period of different sheep breeds and their effects on the growth and development of offspring lambs are still unclear. Hence, this study presents an assessment of the reproductive hormone levels, immune levels, rumen microbiota, and metabolites in Hu sheep and Suffolk ewes at different reproductive periods and their effects on the growth and development of offspring lambs.ResultsHu sheep and Suffolk during non-pregnancy, pregnancy, and lactation were used as the research objects to determine reproductive and immune indexes of ewes at different periods, analyze rumen microbiome and metabolome, and track the growth performance and development of offspring lambs. The results showed that the reproductive hormone and immune levels of Hu sheep and Suffolk underwent adaptive changes across different reproductive periods. Compared with non-pregnancy, the microbial energy metabolism and lipid metabolism function decreased during Hu sheep pregnancy, and energy metabolism function decreased during lactation. In Suffolk, energy metabolism, glycan biosynthesis, and metabolism function were enhanced during pregnancy, and the metabolism of cofactors and vitamins was enhanced during lactation. Prevotella increased in Suffolk during pregnancy and lactation (P < 0.05) and was positively correlated with the birth weight and body size of the lambs (P < 0.05). Moreover, the abundances of Butyrivibrio and Rikenellaceae_RC9_gut_group during pregnancy were positively correlated with the intestinal immunity of the offspring lambs (P < 0.05), thereby regulating the intestinal immunity level of the lambs. Metabolomic analysis revealed that the protein digestion, absorption, and amino acid metabolism of Hu sheep were enhanced during pregnancy, which provided amino acids for the growth and development of pregnant ewes and fetuses and was significantly correlated with the birth weight, body size, and intestinal immunity of lambs (P < 0.05). Simultaneously, there was an increase in acetate and propionate during the pregnancy and lactation period of both Hu sheep and Suffolk, providing energy for ewes during reproductive period. Moreover, the microbiota during the lactation period was significantly correlated with the milk quality and lambs daily gain (P < 0.05).ConclusionsThis study revealed the characteristic succession changes in the rumen microbiota and its metabolites at different reproductive periods in sheep breeds and their regulation of reproductive hormone and immune levels and identified their potential effects on the growth and development of offspring lambs. The findings provide valuable insights into the health and feeding management of different sheep breeds during the reproductive stage.Cnu7uEJBESQuA-vs1kGzfaVideo

Caprine and Ovine Genomic Selection-Progress and Application.

The advancement of sequencing technology and molecular breeding methods has provided technical support and assurance for accurate breeding. Genomic Selection (GS) utilizes genomic information to improve livestock breeding, and it is more accurate and more efficient than traditional selection methods. GS has been widely applied in domestic animal breeding, especially in cattle. However, there are still limited studies on the application and research of GS in sheep and goats. This paper outlines the principles, analysis methods, and influential factors of GS and elaborates on the research progress, challenges, and prospects of applying GS in sheep and goat breeding. Through the review of these aspects, this paper is expected to provide valuable references for the implementation of GS in the field of sheep and goat breeding.

Long-term anthropogenic drivers of diet composition and niche breadth in an endangered avian scavenger: The scant role of sanitary regulations

The widespread and accelerated transformation experienced by our planet results in populations of endangered species having to survive in highly-altered environments and increasingly relying on resources provided by human subsidies. Presently, vultures rank among the most imperiled functional groups of large vertebrates globally, a situation that is largely attributed to the rapid intensification of agriculture and the subsequent transformation of farming practices and agro-grazing landscapes. Hence, documenting the long-term fluctuations in the vultures’ dietary patterns in response to environmental changes, particularly in livestock management, is of utmost significance. Here, by means of bulk stable isotope analysis (δ13C and δ15N), we examined long-term variations in diet composition and niche breadth in a population of the endangered Egyptian vulture (Neophron percnopterus) in the north of the Iberian Peninsula. We specifically focused on the effect of European sanitary regulations enacted in 2014, which allow sheep farmers to abandon livestock remains for consumption by scavenging birds, except for pig carcasses. We found that the implementation of these new regulations did not cause a change in the diet of vultures. Changes were only detected in scrubland areas and were driven by an increase in the consumption of wild rabbit which, in turn, lead to expansion of the trophic niche. These results indicate that these endangered vultures are heavily dependent on food sources derived from intensive farming, mostly of pigs illegally disposed in the wild, and moreover, highlight the importance of carcasses of small vertebrates, often disregarded in conservation programs in favor of the contribution of livestock remains. Our research provides valuable insights into the spatiotemporal dynamics of trophic strategies among avian scavengers, specifically in the context of changes resulting from intensified human-pressures on agro-grazing Mediterranean landscapes.

Genomic selection strategies for the German Merino sheep breeding programme - A simulation study.

Genomic selection is widely implemented in livestock breeding programmes across species. Its potential is also evident for sheep breeding; however, it has several limitations, particularly because of the high genetic diversity across and within sheep breeds. In Germany, the predominant sheep breed is the Merino sheep. Until now, there has been no use of genomic selection in the German Merino sheep breeding programme. In this simulation study, different genomic selection strategies were compared with a reference scenario with a breeding value estimation based on pedigree BLUP. A simplified version of the German Merino sheep breeding programme, including a health and a production trait in the breeding goal, was simulated via the R package Modular Breeding Program Simulator (MoBPS). Real genotype data were used to create a population specific simulation. The reference scenario was compared with several alternative scenarios in which selection was based on single-step GBLUP (ssGBLUP) breeding value estimation with varying genotyping strategies. In addition to scenarios in which all male and all male plus all female lambs were genotyped, scenarios with a preselection of lambs, that is only a certain proportion (top 25%, top 50%) genotyped, were simulated. The results revealed that genetic gain increased with increasing numbers of available genotypes. However, marginal gains decreased with increasing numbers of genotypes. Compared with the reference scenario, genotyping the top 25% of male lambs increased the genetic gain for the breeding ram population by 13% for both traits whereas genotyping the top 50% of male lambs or all male lambs led to increases of 18% (17%) or 26% (21%) for the health (production) trait, respectively. The potential of genotyping females in addition to male lambs was less evident on the male side with no significant differences between the scenarios with different proportions of genotyped females. The results have shown that genomic selection can be a valuable tool to increase genetic gain in the German Merino sheep population and that the genotyping of a certain proportion of animals might lead to substantial improvement over pedigree-based breeding value estimation. Nevertheless, further studies, especially economic evaluations, are needed before practical implementation.

A comprehensive study of CYP2E1 and its role in carcass characteristics and chemical lamb meat quality in different Indonesian sheep breeds.

The role of CYP2E1 in oxidation is essential for its effects on meat quality. This study used 200 Indonesian sheep (Ovis aries) to determine the SNP g allele frequencies. g. 50658168 T>C of CYP2E1 gene located in 3´-UTR region and their genetic association with lamb quality traits, including carcass characteristics, retail cut carcass, physicochemical lamb, fatty acid, cholesterol, flavor and odor, and mineral content. Further, the level of CYP2E1 mRNA and CYP2E1 protein expression in muscle were determined and correlated with lamb quality traits. CYP2E1 gene polymorphisms were identified using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) analysis. The CYP2E1 mRNA expression levels in phenotypically divergent sheep populations were analyzed using Quantitative Real Time-PCR (qRT-PCR). Immunohistochemistry (IHC) and hematoxylin-eosin (HE) staining analysis used three samples each in the high and low lamb quality groups based on pH value and tenderness. An association study of CYP2E1 gene polymorphisms was performed using General Linear Model (GLM) analysis. The genetic association between the CC, CT, and TT genotypes at the SNP g. 50658168 T>C CYP2E1 gene and lamb quality traits were significant (P<0.05), including carcass characteristics, retail cut carcass, fatty acid, cholesterol, flavor, and odor. Lambs with the CT genotype had a higher mRNA and protein expression in high lamb quality traits. The highest CYP2E1 protein expression was localized in the longissimus dorsi. The group sample with high lamb quality had a higher area and perimeter of muscle cells. CYP2E1 can be used as a genetic marker for selecting sheep with high meat quality.

Case report: membranoproliferative glomerulonephritis associated with Q fever causing chronic endocarditis

BackgroundMembranoproliferative glomerulonephritis is a rare entity which can be a result from autoimmune diseases, caused by various medications and infections.Case presentationWe herein present the case of a 62-year-old male patient who presented with fatigue and was found to have severe anemia, impaired renal function, and nephrotic syndrome. A renal biopsy revealed membranoproliferative glomerulonephritis (MPGN) of the immune complex type with activation of the classical complement pathway. Further investigations led to the diagnosis of a chronic Coxiella burnetii-infection (Q fever), likely acquired during cycling trips in a region known for intensive sheep farming. Additionally, the patient was found to have a post endocarditic destructive bicuspid aortic valve caused by this pathogen. Treatment with hydroxychloroquine and doxycycline was administered for a duration of 24 months. The aortic valve was replaced successfully and the patient recovered completely.ConclusionsEarly detection and targeted treatment of this life-threatening disease is crucial for complete recovery of the patient.

Population structure and breed identification of Chinese indigenous sheep breeds using whole genome SNPs and InDels

BackgroundAccurate breed identification is essential for the conservation and sustainable use of indigenous farm animal genetic resources. In this study, we evaluated the phylogenetic relationships and genomic breed compositions of 13 sheep breeds using SNP and InDel data from whole genome sequencing. The breeds included 11 Chinese indigenous and 2 foreign commercial breeds. We compared different strategies for breed identification with respect to different marker types, i.e. SNPs, InDels, and a combination of SNPs and InDels (named SIs), different breed-informative marker detection methods, and different machine learning classification methods.ResultsUsing WGS-based SNPs and InDels, we revealed the phylogenetic relationships between 11 Chinese indigenous and two foreign sheep breeds and quantified their purities through estimated genomic breed compositions. We found that the optimal strategy for identifying these breeds was the combination of DFI_union for breed-informative marker detection, which integrated the methods of Delta, Pairwise Wright's FST, and Informativeness for Assignment (namely DFI) by merging the breed-informative markers derived from the three methods, and KSR for breed assignment, which integrated the methods of K-Nearest Neighbor, Support Vector Machine, and Random Forest (namely KSR) by intersecting their results. Using SI markers improved the identification accuracy compared to using SNPs or InDels alone. We achieved accuracies over 97.5% when using at least the 1000 most breed-informative (MBI) SI markers and even 100% when using 5000 SI markers.ConclusionsOur results provide not only an important foundation for conservation of these Chinese local sheep breeds, but also general approaches for breed identification of indigenous farm animal breeds.

Genome-wide discovery of selection signatures in four Anatolian sheep breeds revealed by ddRADseq

High-density genomic data analyzed by accurate statistical methods are of potential to enlighten past breeding practices such as selection by unraveling fixed regions. In this study, four native Turkish sheep breeds (80 samples) were genotyped via 296.097 single nucleotide polymorphisms (SNPs) detected by double-digest restriction site-associated DNA (ddRADseq) library preparation combined with the Illumina HiSeq X Ten instrument in order to identify genes under selection pressure. A total of 32, 136, 133, and 119 protein-coding genes were detected under selection pressure by runs of homozygosity (ROH), integrated haplotype score (iHS), the ratio of extended haplotype homozygosity (Rsb), and fixation index (FST) approaches, respectively. Of these, a total of 129 genes were identified by at least two statistical models which overlapped with a total of 52 quantitative trait loci (QTL)-associated SNPs, known to be related to fiber diameter, milk content, body weight, carcass traits, some blood parameters, and entropion. A total of six genes under selection pressure were validated by three statistical approaches five of which are of potential to be integrated into animal breeding since they were associated with wool fiber diameter (ZNF208B), behaviors related to neurocognitive development (CBX1 and NFE2L1), adaptation to high-altitude (SDK1), and anxiety causing internal stress (GSG1L). The sixth gene (COPZ1) turned out to play an important role in coping with different types of cancer in mammals. In particular, ROH analysis uncovered significant findings that the Güney Karaman (GKR) had experienced different selection practices than the Akkaraman (AKR) breed. Moreover, some genes specifically under selection in the GKR breed turned out to be associated with olfaction (OR6K6, OR6N1, OR6N2, and OR4C16), survival during the gestation period (PRR15L), and heat stress (CDK5RAP9). The results of this study imply that GKR may become genetically different from the AKR breed at the genome level due to most probably experiencing different adaptation processes occurring in raised climatic conditions. These differences should be conserved to face future challenges, while other native Turkish sheep breeds could be monitored via genome-wide high-density SNP data to obtain deeper knowledge about the effects of natural selection.

Macroscopic and Microscopic Development of the Stomach in Hamdani Crossbred Sheep Fetuses (Ovis aries)

The ruminant stomach is a critical digestive department in terms of converting low-quality feed into high nutrient-value substances. In these animals, there is a compound stomach structure with 4 compartments. Understanding the developmental structure of the stomach at macroscopic and microscopic levels is especially important in terms of nutrition. Türkiye can be considered one of the leading countries in the world in terms of sheep breeding. Our study aimed to investigate macroscopically and microscopically the developmental structures of the stomach of Hamdani crossbred sheep fetuses collected at different gestation periods. For this purpose, a total of 15 fetuses, 5 fetuses each from 3 different periods of pregnancy, were included in the study. The stomachs of the fetuses were dissected simultaneously and their topographic and macroscopic features were determined. After routine histological procedures, the stomachs separated from the body cavities were stained with Hematoxylin &amp;amp; Eosin and Masson Trichrome stains. As a result of the study, macroscopic and microscopic information about fetal development of the stomach was obtained. It was revealed macroscopically and microscopically that the rumen was the largest part of the stomach until the middle of the 2nd period of gestation, and that the abomasum grew rapidly at the end of this period and showed similar characteristics to the adult sheep stomach. The data of the study will contribute to macroscopic, microscopic, and ultrasonographic studies on the stomach in ruminant animals.

Breeding Perspective and Analysis of Utility Parameters of the Suffolk Sheep Breed

Abstract Due to insufficient appreciation for the breeding of dairy sheep, breeds of sheep without market milk production have started to gain popularity in Slovakia. Particularly, meat breeds are coming to the forefront, with their breeding being less demanding and more efficient, reflected mainly in the daily weight gains of growing lambs. Study aimed to analyse the utility and reproductive parameters of breeding the meat breeds Suffolk, located in central Slovakia, in the Rimavská Sobota district. Analysis is supplemented by a detailed description of the breed standard and devotes attention to all the tasks carried out on the farm during the sheep farming year. It focuses mainly on a simple year-round grazing system without housing, utilizing only shelters for protection against adverse weather conditions. Analysed utility and reproductive parameters such as average daily gains, loin muscle thickness, backfat thickness, and fertility were compared and evaluated over the last seven years. Results indicate that the evaluated parameters are mainly influenced by the size of the flock, the number of ewes put to ram, the individual approach to each breeding ewe, and environmental factors. Number of offspring is mainly influenced by the nutrition of the dam in the last third of pregnancy. Despite the simplicity of the breeding system, monitored breeding can achieve above-average results with proper management and innovative approaches.

Investigation of Toxoplasma gondii Infection in Yunnan Semi-fine Wool Sheep (Ovis aries) and wild Rodents in Yunnan, China.

Toxoplasma gondii, a globally distributed zoonotic obligate intracellular parasite, infects a wide array of mammals, including humans, sheep, and birds. As a unique sheep breed in southwestern China, Yunnan semi-fine wool sheep occupies an important position in animal husbandry in Zhaotong due to its strong adaptability, high reproductive rate, and excellent wool quality. Lambs infected with T. gondii are prone to neurological symptoms and growth retardation, while T. gondii infection in ewes can cause abortions, stillbirths, and deformities, thus affecting sheep reproduction and sheep product quality. Meanwhile, mutton and dairy products contaminated with T. gondii can become potential sources of human infection, potentially threatening public health and safety. To understand the T. gondii infection in semi-fine wool sheep in Zhaotong, Yunnan Province, 586 blood samples were collected and subjected to indirect hemagglutination assay (IHA) for T. gondii antibodies, and the infection-related factors were analyzed through cross-sectional analysis. In the meantime, nested PCR was conducted on a total of 217 samples collected from 31 rodents caught in and around the sheep breeding ground to test the T. gondii B1 gene in rodent tissues. A total of 94 sera tested positive for T. gondii antibodies, with a total positive rate of 16.04% (94/586) (95% CI: 14.77-20.89). Cross-sectional statistical analysis on factors related to semi-fine wool sheep infection rate, including sampling season, sex, age, and weight, suggested that age (< 6 months: 23.81%; 6-12 months: 11.74%; > 12 months: 15.83%) was a significant factor explaining the infection rate differences (P = 0.003 < 0.05, χ2 = 11.62, df = 2). Thus, age was considered a key risk factor for T. gondii infection in this study (odds ratio, OR = 2.35, 95% CI: 1.42-3.87). Nested PCR analysis on 217 (heart, liver, spleen, lung, kidney, brain, and muscle) tissues from the 31 rodents indicated that 11 tested positive. The total infection rate of rodents in and around the breeding ground was 35.48% (11/31), and 14 samples tested positive, with a positive infection rate of 6.45% (14/217). The T. gondii infection rates of semi-fine wool sheep and rodents from their breeding environment in Zhaotong, Yunnan Province, were high, necessitating enhanced prevention, control, and treatment measures to ensure the healthy breeding of semi-fine wool sheep and veterinary public health and safety.

Analysis of polymorphism in the TMEM154 gene associated with genetic resistance to Visna Maedi in semi - fine wool sheep breeds

Analysis of polymorphism in the TMEM154 gene associated with genetic resistance to Visna Maedi in semi - fine wool sheep breeds