Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 May 22:12:1545694.
doi: 10.3389/fvets.2025.1545694. eCollection 2025.

Transcriptomics characteristics and differentiation of subcutaneous adipose tissue among Huainan pigs and its hybrid genetic populations

Taotao Yan  1   2 , Mingyang Jia  1 , Jiaxi Li  1 , Xianyong Lan  2 , Liwei Yuan  3 , Baosong Xing  1 , Chuanying Pan  2 , Qingxia Lu  1 , Jing Wang  1
Affiliations

Transcriptomics characteristics and differentiation of subcutaneous adipose tissue among Huainan pigs and its hybrid genetic populations

Taotao Yan et al. Front Vet Sci. .

Abstract

Introduction: The Huainan pig (HN) is known for its impressive litter size and exquisite meat quality. However, it also exhibits certain drawbacks such as excessive fat deposition, a relatively low percentage of lean meat percentage, and a slower growth rate. Crossbreeding with lean-type breeds, such as Large White, Landrace, and Berkshire can enhance offspring traits, and increase genetic diversity.

Methods: In this study we employed RNA-seq technology to identify differentially expressed genes (DEGs) in subcutaneous adipose tissue (SAT) samples from HN pigs and their crosses with multiple breeds (with three replicates per group).

Results: In the SAT of Huainan × Berkshire pigs (BH), Huainan × Yorkshire pigs (YH), and Huainan × Landrace pigs (LH), numerous key functional genes were identified, including LIPG, PLIN2, CPT1A, KLF9, CCND1, LDLR, ACSL1, ACLY and ANGPTL4. Functional enrichment analysis revealed that DEGs were primarily involved in several key pathways in BH, including the peroxisome proliferator-activated receptor (PPAR) signaling, metabolic pathways, arachidonic acid metabolism, and arginine/proline metabolism. Similarly, in LH, DEGs were associated with PPAR, cyclic adenosine monophosphate (cAMP) signaling, mitogen-activated protein kinase (MAPK), and the arginine/proline pathway. In contrast, the main pathways in YH were slightly different, including MAPK, fatty acid elongation, arginine/proline metabolism, and glycine/serine/threonine metabolism. Compared to HN, the differential genes in BH, LH, and YH showed a reduced fat deposition. However, in comparison, LH has a stronger subcutaneous fat deposition ability. Notably, LH exhibited a stronger tendency for subcutaneous fat deposition than the other two groups, while YH had the lowest fat deposition capacity.

Conclusion: In conclusion, these findings offer valuable insights and provide a foundation for future research on the molecular mechanisms underlying fat deposition in pigs.

Keywords: DEGs; Huainan pig; adipose tissue; hybridization; transcriptomics.

PubMed Disclaimer

Conflict of interest statement

LY was employed by Henan Yifa Animal Husbandry Co, Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Comparative analysis of HN and three crosses (BH, LH, YH) in terms of: (A) backfat thickness (mm) measured between the 6th and 7th ribs, (B) marbling score after 24 h, and (C) leaf lard weight. “*” denotes a statistical significance of p < 0.05. “**” denotes a statistical significance of p < 0.05.
Figure 2
Figure 2
Comparison of sequencing reads and distribution of positively expressed genes. (A) The distribution of sequencing reads in the reference genome. The distribution of reads in the exons (red), introns (blue), and intergenic regions (green) are shown. (B) Distributions of expression values of 12 samples. The boxplots show log10 (FPKM + 1) values of each gene from the 4 sets of RNA-Seq data. The black lines in the boxes represent the medians. (C) Pearson correlation coefficients for comparisons among all samples.
Figure 3
Figure 3
Differential gene expression analysis of subcutaneous adipose tissue between different groups. (A) Bar plot of differentially expressed genes in different groups. (B) Venn diagram of DEGs in different groups. (C–E) Volcano plots of Volcano map of DEGs.
Figure 4
Figure 4
Heatmap of differentially expressed genes (DEGs) in subcutaneous adipose tissue across porcine hybrid groups. (A) BH vs. HN; (B) LH vs. HN; (C) YH vs. HN; (D) BH vs. LH vs. YH vs. HN.
Figure 5
Figure 5
Functional enrichment analysis of differentially expressed genes. (A) Gene Ontology (GO) term enrichment; (B) Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment.
Figure 6
Figure 6
GO database enrichment analysis of DEGs: (A,B) LH vs. HN, (C–D) BH vs. HN, (E,F) YH vs. HN.
Figure 7
Figure 7
KEGG enrichment analysis of DEGs. (A) BH vs. HN; (B) LH vs. HN; (C) YH vs. HN.
Figure 8
Figure 8
GESA enrichment analysis of all the DEGs. (A–D) BH vs. HN; (E–H) LH vs. HN; (I–L) YH vs. HN.
Figure 9
Figure 9
Differential expression gene interaction network. (A) BH vs. HN; (B) LH vs. HN; (C) YH vs. HN; (D) The common DEGs shared among the three groups: BH vs. HN, LH vs. HN, and YH vs. HN.
Figure 10
Figure 10
Validation of the DEGs using qRT-PCR. (A–H) qRT-PCR verification of differential gene expression. *p < 0.05, **p < 0.01.
Figure 11
Figure 11
Validation of the DEGs using RNA-seq. (A–F) FPKM values of differentially expressed genes across different groups. *p < 0.05, **p < 0.01.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Wang W, Wang D, Zhang X, Liu X, Niu X, Li S, et al. . Comparative transcriptome analysis of longissimus dorsi muscle reveal potential genes affecting meat trait in Chinese indigenous Xiang pig. Sci Rep. (2024) 14:8486. doi: 10.1038/s41598-024-58971-2, PMID: - DOI - PMC - PubMed
    1. Han Y, Tan T, Li Z, Ma Z, Lan G, Liang J, et al. . Identification of selection signatures and loci associated with important economic traits in Yunan black and Huainan pigs. Genes. (2023) 14:655. doi: 10.3390/genes14030655, PMID: - DOI - PMC - PubMed
    1. Zhang D, Wu W, Huang X, Xu K, Zheng C, Zhang J. Comparative analysis of gene expression profiles in differentiated subcutaneous adipocytes between Jiaxing black and large white pigs. BMC Genomics. (2021) 22:61. doi: 10.1186/s12864-020-07361-9, PMID: - DOI - PMC - PubMed
    1. Chen Q, Zhang W, Cai J, Ni Y, Xiao L, Zhang J. Transcriptome analysis in comparing carcass and meat quality traits of Jiaxing black pig and Duroc × Duroc × Berkshire × Jiaxing black pig crosses. Gene. (2022) 808:145978. doi: 10.1016/j.gene.2021.145978, PMID: - DOI - PubMed
    1. Hang J, Wang J, Ma C, Wang W, Wang H, Jiang Y. Comparative transcriptomic analysis of mRNAs, miRNAs and lncRNAs in the longissimus dorsi muscles between fat-type and lean-type pigs. Biomol Ther. (2022) 12:1294. doi: 10.3390/biom12091294, PMID: - DOI - PMC - PubMed

LinkOut - more resources