A genome-wide association study reveals novel SNP markers associated with resilience traits in two Mediterranean dairy sheep breeds.

Genetic selection for higher productivity increased dairy sheep susceptibility to diseases and environmental stressors, challenging their health and welfare status and production efficiency. Improving resilience to such stressors can enhance their ability to face these challenges without compromising productivity. Our objective was to estimate genomic heritability and perform genome-wide association studies (GWAS) to detect SNPs and candidate genes associated with three proxy traits for resilience (milk somatic cell count-SCC, lactation persistency-LP, body condition score-BCS) of Chios and Frizarta dairy ewes. We used genome-wide genotypes of 317 Chios and 346 Frizarta ewes. Individual records of milk yield and BCS, and milk samples were collected monthly for two consecutive milking periods; samples were analyzed to determine SCC. The LP was calculated as the regression coefficient of daily milk yield on days from lambing. Within breed, variance components analyses and GWAS were performed using genomic relatedness matrices in single-trait animal linear mixed models. Genomic-based heritability estimates were relatively high (BCS: h2 = 0.54 and 0.55, SCC: h2 = 0.25 and 0.38, LP: h2 = 0.43 and 0.45, for Chios and Frizarta ewes, respectively), compared to previous pedigree-based studies. The GWAS revealed 7 novel SNPs associated with the studied traits; one genome-wide and two suggestive significant SNPs for SCC (Frizarta: rs403061409, rs424064526 and rs428540973, on chromosomes 9, 1 and 12, respectively), one suggestive significant SNP for BCS (Chios: rs424834097 on chromosome 4) and three suggestive significant SNPs for LP (Frizarta: rs193632931 and rs412648955 on chromosomes 1 and 6, Chios: rs428128299 on chromosome 3). Nineteen candidate genes were detected: two for BCS (Chios: POT1, TMEM229A), thirteen for SCC (Frizarta: NTAQ1, ZHX1, ZHX2, LOC101109545, HAS2, DERL1, FAM83A, ATAD2, RBP7, FSTL1, CD80, HCLS1, GSK3B) and four for LP (Frizarta: GRID2, FAIM, CEP70-Chios: GRIP1). Present results show that resilience in the studied dairy sheep breeds is heritable and advance existing knowledge on the genomic background of SCC, LP, and BCS. Future research will quantify effects of different alleles of significant SNPs on the studied traits and search for possible correlations among traits to facilitate their effective incorporation in breeding programs aiming to improve resilience.

FarmDain, a Decision Support System for Dairy Sheep and Goat Production.

Managing a milk zone in the dairy industry is demanding. Data necessary for efficient management are difficult to acquire because they usually must be collected in organized and standardized ways. On the other hand, software practices constantly provide new tools that can go beyond simple record-keeping practices and add value to the data. In this work, FarmDain is a novel web-based application for sheep and goat management. It aims to improve milk production and processing by digitizing the value chain in data acquisition, processing and visualization between dairy production businesses and their milk suppliers. FarmDain uses state-of-the-art software technologies to model the data collection process and provides a straightforward user interface to facilitate data processing and visualization. Using the app in a case study carried out for 12 months in a dairy sheep farm resulted in lower feeding cost per milked ewe by 5.5% when ewes were allocated into high and low milk production groups compared to the scenario of remaining in one single group. Furthermore, based on reports provided by the app, culling and genetic selection decisions were made to improve the overall farm performance. Similar practices were applied in all farms optimizing their productivity, which led to increased profitability for farms and the Dairy Factory.

Repeatability of Health and Welfare Traits and Correlation with Performance Traits in Dairy Goats Reared under Low-Input Farming Systems.

The objectives of the study were to estimate the repeatability of health and welfare traits and investigate their association with performance in three breeds of dairy goats reared under low-input farming systems in Greece. A total of 1210 goats of Eghoria (n = 418), Skopelos (n = 429), and Damascus (n = 363) breeds were assessed. Udder health, parasitic resistance, welfare, milk yield and quality, and body condition score were recorded monthly for two milking periods. Udder health records included somatic cell count (SCC) and total viable count (TVC). Based on combinations of SCC and TVC and thresholds set at >106 cells/mL and >2 × 104 cfu/mL, respectively, additional udder health phenotypes were defined. Parasitism included myiasis, tick infestation, gastrointestinal nematode (GIN) and cestode faecal egg count (FEC), and lungworm faecal larval count (FLC). Infection with each of the endoparasites was defined based on FEC/FLC. Welfare assessment parameters included the presence of ear and horn injuries, ocular and nasal discharge, body and udder abscesses, injury and lesions on the skin of different regions, diarrhoea, hernias, overgrown hooves, arthritis, lameness, and udder asymmetry. Trait repeatability and animal correlations were estimated. Significant (p < 0.05) repeatability was reported for all udder health and most welfare traits in all breeds, GIN and cestode FEC, and GIN and lungworm infection in Eghoria, and myiasis in Skopelos. Correlations of health and most of welfare traits with performance were non-significant or favourable. Overall, results demonstrate potential to improve health and welfare of the studied breeds without compromising performance.

Association of Hard Ticks (Ixodidae) Infestation with Milk Production and Udder Health of Extensively Reared Dairy Goats.

Extensively reared ruminants are seasonally exposed to ticks. Tick-related production losses and health issues have been well documented in cows and sheep but not in goats where relevant literature is scarce. The objective here was to investigate the association of hard tick infestation with milk production and udder health of dairy goats reared extensively. A cross-sectional study was carried out during May and June, in two dairy goat farms. The farms were located in Central and Northern Greece and were representative of typical extensive production systems. A total of 304 goats (n = 152 from each farm) were randomly selected. Each goat was examined for presence of hard ticks. Daily milk yield and quality characteristics were recorded. Udder health status was determined by milk somatic cell count (SCC) and total viable count (TVC). Tick infestation prevalence was 28.6%; it was associated with a significant (p < 0.001) increase in SCC and TVC (84.0% and 78.6%, respectively). The latter meant that infested goats were 3.7 times more prone to udder health problems (p < 0.001). There were not any significant effects (p > 0.05) on milk production. Overall, results suggest that control of tick infestation in extensively reared dairy goat herds is important for enhancing health and welfare status.

The Role of Housing Conditions on the Success of Artificial Insemination in Intensively Reared Dairy Ewes in Greece.

The objective was to assess the effect of housing conditions during the summer months on the success rates of cervical artificial insemination (AI) with cooled semen, in intensively reared dairy ewes in Greece. The study involved 2083 Lacaune ewes from 23 flocks that were serviced during May to September. An estrous synchronization protocol with the insertion of progestogen sponges for 14 days and eCG administration at sponge removal, was used. All ewes were inseminated 54−57 h after sponge removal with cooled semen (15 °C) from 10 Lacaune rams. Pregnancy diagnosis was performed via trans-dermal ultrasonography at 35−40 days after AI. Data recording started the day after sponge placement (15 days prior to AI), and lasted up to 14 days after AI. Daily records included temperature, relative humidity, and Temperature-Humidity Index (THI) inside the shed. Available space and volume per animal, frequency of bedding renewal, access to a yard, and indoor light were also recorded in each farm. Binary logistic regression of data records showed that temperature and THI increases at days −15 to +4 around AI (day 0) had a negative effect on pregnancy rates (reducing the likelihood of pregnancy by 3−6% and 7%, respectively). The latter also decreased significantly (p < 0.05) in farms with high stocking density, non-frequent bedding renewal, and outdoor access by ewes (by 30%, 34%, and 44%, respectively). Overall, the results indicate that appropriate housing conditions are warranted to increase the success of AI in dairy ewes during the summer months.

A Comprehensive Study of the Quality of Fat-Tailed Sheep Carcasses in Greece.

Sheep farming in Greece is focused on milk production. Meat is considered a by-product and consists mainly light carcasses of undefined quality. The main challenge of the sector is to ensure sustainability, and hence efforts are towards efficient use of available resources, including undervalued carcasses of local fat-tailed sheep. The objective here was twofold: (i) to assess the carcass quality of fat-tailed sheep slaughtered at different live weights and (ii) to compare them with carcasses from thin-tailed sheep. In total, 146 fat-tailed and 97 thin-tailed dairy sheep were used. They belonged to five live-weight categories (LWC), representing 25%, 35%, 50%, 70% and 100% of mature body weight. Carcass length/weight/yield/pH and wither height were recorded. Muscle fiber minimum Feret's diameter and meat color/tenderness/moisture/lipid and protein content were determined. Sex and LWC differences in fat-tailed sheep were assessed. Parametric and non-parametric tests were used to compare with thin-tailed sheep, considering the effects of LWC, sex and their interactions with sheep population (fat-tailed/thin-tailed). Most traits were significantly different (p < 0.05) between groups of fat-tailed sheep. Carcass yield of fat-tailed sheep was significantly higher compared to thin-tailed (p < 0.01). Interactions of sheep population with LWC or sex affected wither height, carcass pH, meat color and tenderness (p < 0.05). Fat-tailed sheep meat quality is equal or higher compared to thin-tailed. Finishing weights corresponding to 50 and 70% LWC may improve capitalization of fat-tailed carcasses.

Determination of Redox Status in Different Tissues of Lambs and Kids and Their in-between Relationship.

The objective of this study was to assess the resting values of the physiological oxidative stress exhibited by lambs and kids reared in Greece, and the potential correlations between redox biomarker levels in blood and other tissues (liver, diaphragm, quadriceps, psoas major muscle). For this purpose, lambs and kids at different developmental stages (d.s.) were used. The latter corresponded to four live weight categories (LWC), each representing 25%, 35%, 70% and 100% of mature body weight. In each of the above tissues, the levels of five common redox biomarkers were determined: glutathione (GSH), catalase (CAT), total antioxidant capacity (TAC), thiobarbituric reactive substances (TBARS), and protein carbonyls (CARBS). The results revealed that lambs and kids belonging to the 35% LWC had weaker endogenous antioxidant pools, while animals in the 70% and 100% LWC had elevated intrinsic antioxidant defense systems. Blood redox biomarkers were associated with the respective ones measured in the diaphragm, liver, quadriceps, and psoas major of both species. Importantly, TBARS levels in blood of animals in the 25% and 100% LWC are correlated with the TBARS levels in all other tissues tested. Blood antioxidant parameters might be used as potential biomarkers to predict the antioxidant status of tissues that affect meat quality. The latter would facilitate quality assessment prior to slaughter, allowing for timely nutritional interventions that can improve meat products.

Efficiency Analysis as a Tool for Revealing Best Practices and Innovations: The Case of the Sheep Meat Sector in Europe.

The slow adoption of innovations is a key challenge that the European sheep sector faces for its sustainability. The future of the sector lies on the adoption of best practices, modern technologies and innovations that can improve its resilience and mitigate its dependence on public support. In this study, the concept of technical efficiency was used to reveal the most efficient sheep meat farms and to identify the best practices and farm innovations that could potentially be adopted by other farms of similar production systems. Data Envelopment Analysis was applied to farm accounting data from 458 sheep meat farms of intensive, semi-intensive and extensive systems from France, Spain and the UK, and the structural and economic characteristics of the most efficient farms were analyzed. These best farmers were indicated through a survey, which was conducted within the Innovation for Sustainable Sheep and Goat Production in the Europe (iSAGE) Horizon 2020 project, the management and production practices and innovations that improve their economic performance and make them better than their peers.

A Decision Support System for Economically Sustainable Sheep and Goat Farming.

The European sheep and goat sector is characterized by low professionalization and management training. Moreover, it is fragmented in terms of production aims and farming systems. Here, iSAGEDSS, a web-based application allowing dairy and meat small ruminant farmers in different countries to make annual management plans by testing future scenarios, is presented. Data were obtained for the meat sheep (United Kingdom and Spain), dairy sheep (France and Greece) and dairy goat production systems (Greece) from partners of the Innovation for Sustainable Sheep and Goat Production in Europe (iSAGE) project. These were used to set default values and ranges for all important farm parameters in each system and country. An algorithm was developed assessing nutritional management and its impact on production and financial performance. Reports focus on profitability, productivity and environmental sustainability. A case study in three dairy sheep farms in Greece was performed. In each case, an evaluation scenario was created using actual farm data that were compared with the estimated ones. Two scenarios testing management decisions for gross margin maximization and milk pricing fluctuations were created. Application results showed high prediction accuracy for gross margin and production estimation (error of circa 9% and 4%, respectively). Moreover, the ability to promote financial, production and grazing management efficiency was demonstrated.

Genetic profile of scrapie codons 146, 211 and 222 in the PRNP gene locus in three breeds of dairy goats.

Polymorphisms at PRNP gene locus have been associated with resistance against classical scrapie in goats. Genetic selection on this gene within appropriate breeding programs may contribute to the control of the disease. The present study characterized the genetic profile of codons 146, 211 and 222 in three dairy goat breeds in Greece. A total of 766 dairy goats from seven farms were used. Animals belonged to two indigenous Greek, Eghoria (n = 264) and Skopelos (n = 287) and a foreign breed, Damascus (n = 215). Genomic DNA was extracted from blood samples from individual animals. Polymorphisms were detected in these codons using Real-Time PCR analysis and four different Custom TaqMan® SNP Genotyping Assays. Genotypic, allelic and haplotypic frequencies were calculated based on individual animal genotypes. Chi-square tests were used to examine Hardy-Weinberg equilibrium state and compare genotypic distribution across breeds. Genetic distances among the three breeds, and between these and 30 breeds reared in other countries were estimated based on haplotypic frequencies using fixation index FST with Arlequin v3.1 software; a Neighbor-Joining tree was created using PHYLIP package v3.695. Level of statistical significance was set at P = 0.01. All scrapie resistance-associated alleles (146S, 146D, 211Q and 222K) were detected in the studied population. Significant frequency differences were observed between the indigenous Greek and Damascus breeds. Alleles 222K and 146S had the highest frequency in the two indigenous and the Damascus breed, respectively (ca. 6.0%). The studied breeds shared similar haplotypic frequencies with most South Italian and Turkish breeds but differed significantly from North-Western European, Far East and some USA goat breeds. Results suggest there is adequate variation in the PRNP gene locus to support breeding programs for enhanced scrapie resistance in goats reared in Greece. Genetic comparisons among goat breeds indicate that separate breeding programs should apply to the two indigenous and the imported Damascus breeds.

Serological prevalence of Coxiella burnetii in dairy goats and ewes diagnosed with adverse pregnancy outcomes in Greece.

INTRODUCTION: Coxiella burnetii is an obligatory intracellular bacterial pathogen causing the zoonotic disease Q fever. The most common reservoirs of C. burnetii are wild mammals, birds and ticks. Pregnant domestic ruminants infected with this bacterium are also a major source of human infection. MATERIAL AND METHODS: The serological prevalence of C. burnetii in goats and sheep diagnosed with adverse pregnancy outcomes was assessed by undertaking a survey on 800 dairy goats and 800 dairy ewes reared in four different regions of Greece (Macedonia, Thrace, Thessaly, and Peloponnese). A stratified sampling was carried out, taking also as a criterion the age of the animals. Serum antibodies were analyzed by a commercial ELISA according to the manufacturer's recommendations. RESULTS: Generally, there was a statistically significantly higher serological prevalence of C. burnetii (14.4%) in goats compared to sheep (8%). Serological prevalence was higher in adults (15.5% in goats and 8.5% in sheep) compared to yearlings (7.4% in goats and 4.6% in sheep). The prevalence increased significantly with age only in goats. Finally, all animals reared in Peloponnese had a prevalence significantly higher (21% in goats and 18% in sheep) than animals reared in the other three regions. CONCLUSIONS: To the best of the authors' knowledge, this is the first report that associates C. burnetii with reproductive disturbances of domestic ruminants in Greece. However, considering the importance of coxiellosis for public health, further investigations are required on its epidemiology regarding abortion, premature delivery, stillbirth and weak offspring in small ruminants, as well as in other domestic and wild animal species.