Transcriptomic Profiling of Adipose Tissues in Sujiang Pigs Reveals Candidate Genes Associated with Tissue-Specific Fat Deposition

Figures

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  Figure 1. PCA results for BF, GOM, and MAD. Note: (A) Three-dimensional PCA scatter plot showing the spatial distribution of all samples along PC1, PC2, and PC3, which account for 34.64%, 18.24%, and 12.24% of the total variance, respectively. BF (red squares), MAD (green triangles), and GOM (blue circles) are distinguished by both color and shape; (B) Two-dimensional PCA scatter plot, representing the projection (top view) of the 3D plot in (A) onto the PC1-PC2 plane, to better visualize the group separation along the first two principal components. The color, shape, and grouping of samples are identical to those in (A).The scales on all axes represent relative distances among samples and do not have absolute meaning. Each point corresponds to one sample, and samples within the same group are shown in the same color.

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  Figure 2. Volcano plot of differentially expressed genes between groups. Note: (A) Volcano plot showing differentially expressed genes in the SJ-BF vs. SJ-GOM comparison. The x-axis indicates log2(Fold Change), and the y-axis represents −log10(qValue). Red, blue, and gray dots correspond to significantly upregulated, significantly downregulated, and non-significantly expressed genes, respectively, with q Value = 0.05 as the significance threshold; (B) Volcano plot of differentially expressed genes from the SJ-BF vs. SJ-MAD pairwise comparison, with axes, gene color coding and significance threshold identical to panel (A); (C) Volcano plot displaying differentially expressed genes identified in the SJ-GOM vs. SJ-MAD comparison, with axes, gene color coding and significance threshold identical to panel (A).

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  Figure 3. Differential gene Venn diagram. Note: Different comparison groups are represented by different colors, and the numbers in the figure represent the number of differentially expressed genes that are unique or shared. The overlapping areas represent the number of differentially expressed genes shared among different comparison groups, while the non-overlapping areas represent the number of differentially expressed genes unique to each comparison group.

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  Figure 4. RT-qPCR verification results of DEGs. Note: The images show the comparison results of the BF-GOM and GOM-MAD groups, respectively. The left axis shows the log2 (fold change) of the RT-qPCR results, and the right axis shows the log2 (fold change) of the RNA-seq data. The pink bars represent the RT-qPCR data, the blue line with circles represents the RNA-seq results of BF-GOM, and the blue line with squares represents the RNA-seq results of GOM–MAD. Red asterisks indicate statistical significance of gene expression differences in RT-qPCR, and blue asterisks indicate statistical significance of gene expression differences in RNA-seq. * p < 0.05 ** p < 0.01 *** p < 0.001.

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  Figure 5. GO enrichment analysis results. Note: (A) GO enrichment analysis of DEGs from the SJ-BF vs. SJ-GOM comparison. The vertical axis displays enriched GO term names, and the horizontal axis shows the count of enriched genes. Red, blue and green bars represent biological process (BP), cellular component (CC), and molecular function (MF) categories, respectively; (B) GO enrichment analysis of DEGs from the SJ-BF vs. SJ-MAD pairwise comparison, with axis settings, color coding for GO categories and plotting criteria identical to panel (A); (C) GO enrichment analysis of DEGs identified in the SJ-GOM vs. SJ-MAD comparison, with axis settings, color coding for GO categories and plotting criteria identical to panel (A).

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  Figure 6. KEGG pathway analysis. Note: (A) KEGG enrichment bubble plot of DEGs from the SJ-BF vs. SJ-GOM comparison. The horizontal axis shows Rich factor, the vertical axis displays pathway names. Dot size corresponds to the number of enriched differential genes, and dot color represents −log10(p value) to reflect enrichment significance; (B) KEGG enrichment bubble plot of DEGs from the SJ-BF vs. SJ-MAD pairwise comparison, with axis definitions, dot size and color coding consistent with panel (A); (C) KEGG enrichment bubble plot of DEGs identified in the SJ-GOM vs. SJ-MAD comparison, with axis definitions, dot size and color coding consistent with panel (A).

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  Figure 7. PPI network of differentially expressed genes associated with lipid metabolism and fat metabolism. Note: (A,C) Global PPI interaction networks from two comparison groups. The greater its importance in the network; the thicker the connection between nodes, the higher the confidence in the gene-gene interaction. light blue nodes highlight the regions where screened potential hub genes are located; (B,D) Corresponding core gene screening subnetworks extracted from panels (A) and (C), respectively, with red circles highlighting the screened potential key genes.