## 4 Discussion  
In this work, we studied the sheep and goat breeds present in small ruminant farms in Greece and we evaluated possible differences between the breeds in SCC and TBC. Farms from all regions of the country were included into the study; hence, conditions prevailing throughout Greece had been taken into account and regional factors had a smaller influence. Figure 4: Proportion of herds with increased somatic cell counts (\(>\)0.75 \(\times\) 10\({}^{6}\) cells mL\({}^{-1}\)) in the bulk-tank milk of goat herds in Greece in accordance with the breed of goats therein. \begin{table}
\begin{tabular}{c c c} \hline \hline \multirow{2}{*}{**Variables (\(n=2\))**} & **Odds Ratio 1** & \\  & **(95\% Confidence Intervals)** & \(p\) \\ \hline Breed & & 0.042 \\ Alpine (\(n=9\)) & 1.125 (0.183–6.935) & 0.90 \\ Damascus (\(n=18\)) & 5.850 (1.222–27.995) & 0.027 \\ Indigenous Greek (_Capra prisca_) (\(n=50\)) & 9.000 (2.295–35.296) & 0.002 \\ Murciana-Granadina (\(n=18\)) & reference & \\ \hline Management system & & 0.01 \\ Intensive (\(n=7\)) & reference & \\ Semi-intensive (\(n=22\)) & 3.611 (0.570–22.898) & 0.17 \\ Semi-extensive (\(n=43\)) & 5.769 (0.988–33.677) & 0.05 \\ Extensive (\(n=18\)) & 12.500 (1.600–97.650) & 0.016 \\ \hline \hline \end{tabular} 1  
\end{table} 
Table 5: Results of multivariable analysis for increased somatic cell counts (\(>\)0.75 \(\times\) 10\({}^{6}\) cells mL\({}^{-1}\)) in the bulk-tank milk of goat herds in Greece (mixed effects logistic regression and analysis with only herds with the four most frequently recorded breeds). Additionally, during the study, we employed consistent methodologies for sampling and sample processing, whilst the same investigators performed specific tasks and always maintained consistency, which all helped to minimize possible bias. Sheep and goat milk are important agricultural products in Greece, and the country produces approximately 25% of the total European small ruminant milk. However, the possible association of the sheep and goat breeds prevalent in the country in the quality of milk have not been hitherto described. A significant proportion of the breeds in the farms was imported breeds. This indicates the continuous efforts of farmers to improve the genetic material in their flocks/herds and to achieve better production, with special reference to milk production. It is noteworthy that all imported breeds are characterized for high milk yield. This was reflected in the higher average milk production achieved in those farms than in farms with breeds of Greek origin. Consequently, this could also be seen in the management system applied in the farms; higher milk production requires increased input into farms: infrastructures (e.g., installation of milking systems), reduced grazing, increased staff numbers, etc., all of which are in line with the intensive or semi-intensive management system. For SCC, as the current EU legislation does not provide a legal threshold, we employed the threshold of 0.75 \(\times\) 10\({}^{6}\) cells mL\({}^{-1}\), following the relevant US regulations and taking into account that dairy factories in the country use this threshold to regulate payments to farmers according to the quality of milk delivered. A similar practice is also applied in Spain, where payments for milk by dairy factories similarly depend upon the SCC therein [25]. For sheep, genomic selection has been shown to have good accuracy for mastitis resistance [26] but only when predicting resistance in closely related animals [27]. In the present study, it was found that breed was of significance for increased SCC, i.e., above the threshold of 0.75 \(\times\) 10\({}^{6}\) cells mL\({}^{-1}\). In Lacaune-breed sheep, a long-standing program for improvements in the resistance to mastitis has been running for over 15 years now [8; 28]. The development of genomic methods and tools for applications to sheep and the sequencing of the sheep genome [29] have greatly contributed in those efforts [13; 30]. In a recent study, [PERSON] et al.