## 3 Results and Discussion
### Effects of Characteristic Bioactive Metabolites on Meat Quality Traits
Figure 3: Correlation analysis between characteristic bioactive compounds and meat quality in the breast muscle of Silkie chickens. Red circles represent a significant positive correlation (\(r>0.3\) and \(p<0.05\)) and blue circles represent a significant negative correlation (\(r<-0.3\) and \(p<0.05\)). Effects of Characteristic Bioactive Metabolites, Lipids, and Fatty Acids on Characteristic Volatiles  
A total of 147 volatile flavor compounds were identified and semi-quantified from the breast muscles of 30 Silkie chickens and 30 Wuding chickens. Figure 4A presents the categories and proportions of volatile flavor compounds, with aldehydes accounting for the highest proportion. The PLS-DA model clearly distinguished between Silkie and Wuding chickens based on these 147 volatile flavor compounds (Figure 4B). Based on the criteria of VIP > 1 and \(p\) < 0.05, eight volatile flavor compounds were significantly upregulated and 24 volatile flavor compounds were significantly downregulated in Silkie chickens (Figure 4C and Table S6). It is worth noting that the upregulated volatiles were mainly aromatic compounds and phenols and the downregulated volatiles were mainly aldehydes and hydrocarbons. Then, we conducted correlation analysis on eight upregulated volatiles and characteristic bioactive compounds (Figure 4D and Table S7). Furfural was positively correlated with D-arabinose and DHA. Phenol was positively correlated with Glu-Thr. 5-Ethyl-2,4-dimethylthiazole was positively correlated with four dipeptides. Previous studies support these correlations. The main pathways for furfural formation include the Maillard reaction induced by saccharides and nitrogenous compounds [58] and the conversion of polyunsaturated fatty acids [59]. Phenols are mainly derived from amino acid degradation [60]. 5-Ethyl-2,4-dimethylthiazole is mainly formed by nonenzymati  
Figure 4: Effects of characteristic bioactive compounds on meat flavor. (**A**) Classification and percentage of volatile flavor compounds. (**B**) PLS-DA based on overall volatile flavor compounds. (**C**) The number of differential volatile flavor compounds in each class. Orange and green represent volatile flavor compounds that were significantly upregulated and downregulated in Silkie chickens, respectively. (**D**) Correlation analysis of eight upregulated volatiles and characteristic bioactive compounds. Red circles indicate a significant positive correlation (r > 0.4 and \(p\) < 0.05). tween reducing sugars and amino acids [61]. The above results indicated that characteristic bioactive metabolites, lipids, and fatty acids may play important roles in the formation of characteristic volatiles in the breast muscle of Silkie chickens. Identification of Key DEGs Involved in Synthesis of Characteristic Bioactive Metabolites, Lipids, and Fatty Acids  
We performed transcriptome sequencing on the breast muscle tissues of 30 Silkie chickens and 30 Wuding chickens, and the two breeds could be well separated based on gene expression levels (Figure 5A). Through further differential analysis, we identified 504 DEGs (fold change \(\geq\) 2 and \(p\) < 0.05), including 212 upregulated and 292 downregulated genes, in Silkie chickens (Figure 5B and Table S8). The results of our GO enrichment analysis and KEGG pathway enrichment analysis of upregulated genes are shown in Figure 5C. The GO database was used to annotate and enrich DEGs in the biological process, cellular component, and molecular function categories. In the biological process category, we noticed that in addition to the significant upregulation of \"melanin biosynthetic process\" and \"melanosome organization,\" \"lipid transport\" was also significantly upregulated in Silkie chickens. We present a biochemical pathway map that visually demonstrates how key DEGs regulate the significant upregulation of characteristic metabolites in Silkie chickens (Figure 6). Characteristic bioactive metabolites and 15 DEGs were enriched in five amino acid pathways, two nucleotide pathways, and one lipid pathway.