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. 2023 Feb 15;24(4):3947.
doi: 10.3390/ijms24043947.

Transcriptomics and Selection Pressure Analysis Reveals the Influence Mechanism of PLIN1 Protein on the Development of Small Size in Min Pigs

Qiao Liu  1 , Liqun Yu  1   2 , Ziwen Zhang  1 , Yang Chang  1 , Zhonghua Liu  1 , Chunzhu Xu  1
Affiliations

Transcriptomics and Selection Pressure Analysis Reveals the Influence Mechanism of PLIN1 Protein on the Development of Small Size in Min Pigs

Qiao Liu et al. Int J Mol Sci. .

Abstract

Body size is an important biological phenotypic trait that has attracted substantial attention. Small domestic pigs can serve as excellent animal models for biomedicine and also help meet sacrificial culture needs in human societies. Although the mechanisms underlying vertebral development regulating body size variation in domestic pigs during the embryonic period have been well described, few studies have examined the genetic basis of body size variation in post embryonic developmental stages. In this study, seven candidate genes-PLIN1, LIPE, PNPLA1, SCD, FABP5, KRT10 and IVL-significantly associated with body size were identified in Min pigs, on the basis of weighted gene co-expression network analysis (WGCNA), and most of their functions were found to be associated with lipid deposition. Six candidate genes except for IVL were found to have been subjected to purifying selection. PLIN1 had the lowest ω value (0.139) and showed heterogeneous selective pressure among domestic pig lineages with different body sizes (p < 0.05). These results suggested that PLIN1 is an important genetic factor regulating lipid deposition and consequently affecting body size variation in pigs. The culture of whole pig sacrifice in Manchu during the Qing Dynasty in China might have contributed to the strong artificial domestication and selection of Hebao pigs.

Keywords: Min pig; WGCNA; body size variation; sacrificial culture; selection pressures.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Co-expressed gene modules detected by weighted gene co-expression network analysis (WGCNA). (A) Cluster dendrogram showing the co-expression modules defined by WGCNA and labeled by colors. (B) Module-trait relationships showing the correlation between gene module and sample information, where the x-axis represents sample information, and the y-axis represents each gene module. In the panel, the darker the color, the higher the correlation, with red representing positive correlation and blue representing negative correlation. Significance values expressed as p-values are in parentheses. (C) Module membership and gene significance relationships of each module. (D) Scatterplot of Gene Significance (GS) for body type vs. Module Membership (MM) in yellow module.
Figure 2
Figure 2
Co-expressed genes in yellow module. (A) The top 20 Gene Ontology (GO) terms identified with yellow module genes. (B) Pie chart of all significant pathways (Q-value < 0.05) in the yellow module. Each sector of the pie chart is proportional to the number of genes in the pathway.
Figure 3
Figure 3
Validation of RNA-seq data by qRT-PCR. The line graph represents the FPKM value of RNA sequencing, and the bar graph represents the relative quantitative results of qRT-PCR.
Figure 4
Figure 4
Hub genes in the yellow module. (A) Network visualization of the co-expression of 25 hub genes in yellow module. (B) The intersection in the Veen map is the most important candidate genes by various analysis methods.
See this image and copyright information in PMC

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