Fig 1.
Physiological differences and high-throughput sequencing strategy were presented in two Chinese Taihe Black-bone chickens.
(A) The appearance characteristics of Black-Bone silk fowl chicken (BB-sfc) and Black-Bone and black-feathered chicken (BB-bfc). (B) Representative images of egg differences between BB-sfc and BB-bfc chickens. (C) Representative images of muscle differences between BB-sfc and BB-bfc chickens. (D) Workflow of high-throughput transcriptome and quantitative proteome analysis of chicken muscle using RNA-Seq and TMT-based LC-MS/MS methods.
Fig 2.
The differentially expressed genes of the Taihe silky fowl chicken in muscle samples were identified by transcriptome analysis.
(A) The volcano plot represented the DEGs identified in the BB-sfc compared with BB-bfc chicken breeds using the DESeq2 method. The X-axis means the change of gene multiplicity (log2 FoldChange), and the Y axis indicates the significance level of the difference (-log10 Adjust P-value). The red and blue dots showed the significantly up- and down-regulated DEGs, respectively. (B) The heatmap of DEGs between BB-sfc and BB-bfc breed chickens was performed by hierarchical clustering analysis. (C) RNA libraries of BB-sfc and BB-bfc presented obvious differences by two-dimensional PCA analysis. (D) The integrated network presented the interaction relationship of DEGs in Taihe Black-bone silky fowl chicken.
Table 1.
Basic statistical characteristics of RNA sequencing in chicken muscle samples.
Fig 3.
GO enrichment and KEGG pathway analysis of up- and down-regulated genes in Taihe silky fowl chicken using RNA-Seq.
(A) The GO enrichment bar graphs for the top 30 items in the up-regulated genes in Taihe silky fowl chicken. (B) The GO enrichment bar graphs for the top 30 items in the down-regulated genes in Taihe silky fowl chicken. Abbreviations: biological processes (BP), cellular components (CC) and molecular functions (MF). (C) The 20 most significant KEGG pathways were identified in significantly up-regulated genes between BB-sfc and BB-bfc chickens. (D) The 20 most significant KEGG pathways were identified in significantly down-regulated genes between BB-sfc and BB-bfc chickens.
Fig 4.
The differential protein screening in Taihe silky fowl chicken using the TMT-based proteomic analysis.
(A) Protein identification and quantitative result statistics in proteomic analysis. (B) Volcano map showing the significant proteins differences on muscles between BB-sfc and BB-bfc chicken breeds. (C) Profiles of different expressed proteins in Taihe silky fowl chicken using the hierarchical clustering analysis. The red presents the significantly up-regulated and blue presents the down-regulated proteins, respectively.
Fig 5.
The functional enrichment and network analysis of DEPs in Taihe silky fowl chicken.
(A) Pie chart shows the number and distribution proportion of proteins in each sub-cellular organ. (B) Interaction networks of differentially abundant proteins in Taihe silky fowl. (C) Representive GO annotation of differentially abundant proteins for biological processes, molecular functions and cellular components, respectively. (D) KEGG pathway enrichment analysis. The vertical axis represents KEGG pathways and the horizontal axis represents the number of differentially expressed proteins in each pathway.
Fig 6.
The integrated transcriptome and proteome analysis identified the specific muscle components in Tailhe silky fowl chicken.
(A) Venn diagram of up-regulated differentially expressed transcripts and proteins in Taihe silky fowl chicken. (B) Venn diagram of down-regulated differentially expressed transcripts and proteins in Taihe silky fowl chicken. (C) The statistical table in the fold-change and significance differences in genes and proteins that commonly up-regulated and down-regulated on the muscle tissues in Taihe silky fowl chicken.