Table 1.
qRT-PCR primer information. (β -actin is an internal control gene).
Fig 1.
Characterization of proteins from HS and YY longissimus dorsi muscle samples.
(A) Overview information of identified proteins in this study. (B) Distribution of the molecular weights of the identified proteins. (C) Distribution of the lengths of the identified peptides.(D) Distribution of the numbers of identified proteins containing different numbers of peptides.(E) The heatmap of clustering analysis illustrates the correlation between HS and YY samples.
Fig 2.
Differentially expressed proteins (DEPs) between the HS and YY pig’s groups.
(A) bar char plot of proteins in the HS and YY pig’s groups. (B) Volcano plot of proteins in the HS and YY pig’s groups. (C)Protein Expression Pattern Analysis. The expression values of DEPs, represented as log₂FC, were utilized as input for cluster analysis. Red indicates proteins up-regulated in both HS and YY pigs, while blue signifies proteins down-regulated in both breeds. (D)Venn diagram of differential proteins (E) Subcellular localization chart of DEPs.
Fig 3.
Functional enrichment profiles in HS vs. YY groups.
(A)GO enrichment analysis of significant DEPs between HS and YY groups. (B)KEGG pathway enrichment analysis of significant DEPs between HS and YY groups.
Fig 4.
Protein-protein interaction (PPI) network of DEPs.
Red nodes represent upregulated proteins, and Green nodes represent downregulated proteins. The size of each node reflects its degree of connectivity, with larger nodes indicating higher interaction degrees.
Fig 5.
The results of RNA-Seq analysis were verified by qRT-PCR technology.
Fig 6.
The results of DIA proteomics analysis were verified by using parallel reaction monitoring (PRM) technology.
Fig 7.
Integrated Analysis of Transcriptome-Proteome Coordination and Functional Enrichment in HS vs. YY Groups (A) Nine-quadrant analysis of transcriptome-proteome coordination in HS vs. YY groups.
(B) GO enrichment analysis of biological processes in HS vs. YY groups. (C) KEGG pathway enrichment analysis in HS vs. YY groups.