# Assessment of Milk Quality in Skopelos Goats Under Low- and High-Input Farming Systems
## 3 Results
### Principal Component Analysis (PCA)
(**b**) Displays the distribution of individual samples across the two principal components, with the extensive and intensive systems color-coded. cos2 values, represented by the color gradient, indicate how well each variable is explained by Dim1 and Dim2. (**c**) Heatmap of Pearson’s correlation coefficients among milk quality, composition, and production traits. Correlation values are displayed only in cells where the relationships are statistically significant (_p_ < 0.05). Blank cells indicate non-significant correlations. The color scale represents the strength and direction of the correlation, with blue tones indicating positive correlations and red tones indicating negative correlations. the lowest average levels across most milk quality indicators. In terms of farming system distribution (Figure 2b), cluster 2 was predominantly composed of samples from extensive systems (93.62%), whereas cluster 3 had a more balanced representation (61.58% extensive, 38.42% intensive). Cluster 1 also included mostly extensive system samples (75.8%) but with a higher proportion of intensive farms (24.2%) compared with cluster 2. These findings indicate an association between farming system and milk composition, with extensive systems linked to higher milk solids but also higher SCC and TBC levels, underscoring a compromise between milk quality and udder health that should be considered in management decisions. Effect of Farming System and Lactation Stage on Milk Yield and Composition Across the Two Lactation Periods  
The results from the linear mixed-effects model examining the effects of the farming system on morning milk yield (am_MY) and milk composition indicate that only certain parameters were significantly affected (Figure 3). Specifically, am_MY was significantly higher in the intensive system (0.98 kg/day) compared with the extensive system (0.85 kg/day) (\(p<0.01\)). In contrast, protein content was significantly higher in the extensive system (3.57%) than in the intensive system (3.47%) (\(p<0.001\)), and similar results were observed for Cas content (2.72% vs. 2.57%, \(p<0.001\)). However, no significant differences were found between farming systems for fat (4.76% vs. 4.75%) or lactose content (4.58% vs. 4.57%), indicating that farming conditions did not influence these components. Regarding the effect of the LS (Figure 4), a highly significant impact was observed on all analyzed milk parameters (\(p<0.001\)). Specifically, the average milk yield (am_MY) peaked during the first LS (1.05 kg/day) and then declined progressively through the second (0.96 kg/day), third (1.01 kg/day), and fourth stages (0.67 kg/day). Fat content (Figure 4b) increased slightly but significantly in the second LS (4.83%), while values in the first, third, and fourth stages remained relatively stable (4.69-4.78%; \(p<0.05\)). Protein content was highest in early lactation (3.58%) and showed a marked decrease by the third (3.43%) and fourth LSs (3.51%) (\(p<0.001\)). Lactose followed a similar downward trend, dropping from 4.74% in the first LS to 4.42% in late lactation (\(p<0.001\)). Both TSs and casein content were significantly influenced by LS, with concentrations highest during early lactation and consistently declining across later stages (\(p<0.001\)), highlighting the dynamic nature of milk composition over time. Figure 2: (a) Distribution of milk traits across clusters; (b) Distribution of farming systems across clusters. Significant interactions were also observed between the year and LS within each farming system. Figure 5 highlights the differences in milk composition at specific LS between the two years within each system. In the extensive system, am_MY (Figure 5a) exhibited a significant decline (\(p<0.001\)) across LSs, with the highest production recorded in the first LS (1.09 kg in 2022, 0.99 kg in 2023) and the lowest in the fourth LS (0.34 kg in 2022, 0.61 kg in 2023). When comparing lactation curves between the two years, no significant difference was observed in the first LS.