Over the recent years, next generation sequencing and microarray technologies have revolutionized scientific research with their applications to high-throughput analysis of biological systems. Isolation of high quantities of pure, intact, double stranded, highly concentrated, not contaminated genomic DNA is prerequisite for successful and reliable large scale genotyping analysis. High quantities of pure DNA are also required for the creation of DNA-banks. In the present study, eleven different DNA extraction procedures, including phenol-chloroform, silica and magnetic beads based extractions, were examined to ascertain their relative effectiveness for extracting DNA from ovine blood samples. The quality and quantity of the differentially extracted DNA was subsequently assessed by spectrophotometric measurements, Qubit measurements, real-time PCR amplifications and gel electrophoresis. Processing time, intensity of labor and cost for each method were also evaluated. Results revealed significant differences among the eleven procedures and only four of the methods yielded satisfactory outputs. These four methods, comprising three modified silica based commercial kits (Modified Blood, Modified Tissue, Modified Dx kits) and an in-house developed magnetic beads based protocol, were most appropriate for extracting high quality and quantity DNA suitable for large-scale microarray genotyping and also for long-term DNA storage as demonstrated by their successful application to 600 individuals.

The aim was to assess the intensified dairy sheep farming systems of the Chios breed in Greece, establishing a typology that may properly describe and characterize them. The study included the total of the 66 farms of the Chios sheep breeders' cooperative Macedonia. Data were collected using a structured direct questionnaire for in-depth interviews, including questions properly selected to obtain a general description of farm characteristics and overall management practices. A multivariate statistical analysis was used on the data to obtain the most appropriate typology. Initially, principal component analysis was used to produce uncorrelated variables (principal components), which would be used for the consecutive cluster analysis. The number of clusters was decided using hierarchical cluster analysis, whereas, the farms were allocated in 4 clusters using k-means cluster analysis. The identified clusters were described and afterward compared using one-way ANOVA or a chi-squared test. The main differences were evident on land availability and use, facility and equipment availability and type, expansion rates, and application of preventive flock health programs. In general, cluster 1 included newly established, intensive, well-equipped, specialized farms and cluster 2 included well-established farms with balanced sheep and feed/crop production. In cluster 3 were assigned small flock farms focusing more on arable crops than on sheep farming with a tendency to evolve toward cluster 2, whereas cluster 4 included farms representing a rather conservative form of Chios sheep breeding with low/intermediate inputs and choosing not to focus on feed/crop production. In the studied set of farms, 4 different farmer attitudes were evident: 1) farming disrupts sheep breeding; feed should be purchased and economies of scale will decrease costs (mainly cluster 1), 2) only exercise/pasture land is necessary; at least part of the feed (pasture) must be home-grown to decrease costs (clusters 1 and 4), 3) providing pasture to sheep is essential; on-farm feed production decreases costs (mainly cluster 3), and 4) large-scale farming (feed production and cash crops) does not disrupt sheep breeding; all feed must be produced on-farm to decrease costs (mainly cluster 3). Conducting a profitability analysis among different clusters, exploring and discovering the most beneficial levels of intensified management and capital investment should now be considered.

The objectives of this study were (1) to record the major pathogens associated with subclinical mastitis (SCM), (2) to calculate their incidence during the milking period, and (3) to estimate the effect of SCM on daily milk yield (DMY) for goats reared under low-input management schemes. Dairy goats (n=590) of Skopelos and indigenous Greek breeds from 4 herds were randomly selected for the study. The study included monthly monitoring, milk yield recording, and bacteriological analyses of milk of individual goats during the course of 2 successive milking periods. Incidence and cumulative incidence were calculated for SCM cases. Moreover, 2 mixed linear regression models were built to assess the effects of (1) SCM and (2) different pathogens isolated from SCM cases, on DMY. The estimated incidence and cumulative incidence of SCM for the first and the second year of the study were 69.5 and 96.4 new cases of SCM/1,000 goat-months, and 24.1 and 31.7%, respectively. A total of 755 milk samples were subjected to microbiological examination, resulting in 661 positive cultures. Coagulase-negative and coagulase-positive staphylococci were isolated from 50.2 and 34.5% of the positive cultures, respectively. The incidence of infections (new infections per 1,000 goat-months) for the first and the second year of the study were 34 and 53 for coagulase-negative staphylococci, 23 and 28 for coagulase-positive staphylococci, 3 and 5 for Streptococcus/Enterococcus spp., and 5.5 and 9.1 for gram-negative bacteria. Goats with SCM had lower DMY when compared with goats without SCM (ca. 47g/d, corresponding to a 5.7% decrease in DMY). In particular, goats with SCM due to coagulase-positive staphylococci infection produced approximately 80g/d less milk (a reduction of ca. 9.7%) compared with uninfected ones, whereas SCM due to gram-negative bacteria resulted in approximately 15% reduction in DMY. Investigating the epidemiology of SCM and its effects on production traits is critical for the establishment of effective preventive measures against SCM and for the assessment of the sustainability of production in low-input dairy goat herds.