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CUI Shengdi, WANG Shujie, ZHAO Zhenjian, et al. Liver RNA-seq reveals key genes and molecular pathways regulating the social genetic effects of residual feed intake in Duroc pigs[J]. Journal of South China Agricultural University, 2025, 46(3): 336-341. DOI: 10.7671/j.issn.1001-411X.202407006
Citation: CUI Shengdi, WANG Shujie, ZHAO Zhenjian, et al. Liver RNA-seq reveals key genes and molecular pathways regulating the social genetic effects of residual feed intake in Duroc pigs[J]. Journal of South China Agricultural University, 2025, 46(3): 336-341. DOI: 10.7671/j.issn.1001-411X.202407006

Liver RNA-seq reveals key genes and molecular pathways regulating the social genetic effects of residual feed intake in Duroc pigs

More Information
  • Received Date: July 02, 2024
  • Available Online: February 26, 2025
  • Published Date: March 02, 2025
  • Objective 

    This study aims to elucidate the molecular regulatory mechanisms of the social genetic effects of residual feed intake (SGE-RFI) in Duroc pigs, and reveal the biological basis of how it influences group behavior through energy metabolism pathways, thereby providing a theoretical basis for improving feed utilization efficiency in pigs.

    Method 

    By employing RNA sequencing technology, a comprehensive transcriptome analysis of the liver tissue in Duroc pigs was conducted, systematically screening for key differentially expressed genes related to the SGE-RFI trait. Functional enrichment methods were used to analyze the biological pathways involved.

    Result 

    The study identified 360 significantly differentially expressed genes. Functional analysis indicated that these genes were primarily enriched in energy-related pathways such as mitochondrial oxidative phosphorylation and ATP metabolism, suggesting an indirect influence on social behavior through the regulation of energy homeostasis. The coordinated expression changes in the apolipoprotein gene cluster APOA1, APOC3 and APOA4 revealed the interaction between the neuroendocrine system and lipid metabolism during the social genetic effect regulation.

    Conclusion 

    This research has constructed a multi-dimensional regulatory network for SGE-RFI in Duroc pigs, offering not only a new perspective for understanding the genetic mechanisms of group behavior, but also laying a molecular foundation for the precise selection of breeding pigs with low residual feed intake and the optimization of group feeding management strategies.

  • [1]
    VIGORS S, O'DOHERTY J V, BRYAN K, et al. A comparative analysis of the transcriptome profiles of liver and muscle tissue in pigs divergent for feed efficiency[J]. BMC Genomics, 2019, 20(1): 461. doi: 10.1186/s12864-019-5740-z
    [2]
    IBRAGIMOV E, PEDERSEN A, XIAO L, et al. Analysis of merged transcriptomic and genomic datasets to identify genes and pathways underlying residual feed intake in growing pigs[J]. Scientific Reports, 2022, 12(1): 21946. doi: 10.1038/s41598-022-26496-1
    [3]
    LIU H, FEYE K M, NGUYEN Y T, et al. Acute systemic inflammatory response to lipopolysaccharide stimulation in pigs divergently selected for residual feed intake[J]. BMC Genomics, 2019, 20(1): 728. doi: 10.1186/s12864-019-6127-x
    [4]
    禹世欣, 王书杰, 赵真坚, 等. 杜洛克猪剩余采食量的社会遗传效应与其他经济性状的关联分析 [J]. 中国畜牧杂志, 2024, 60(8): 141-145.
    [5]
    ZHANG Y, PARK C, BENNETT C, et al. Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N[J]. Genome Research, 2021, 31(7): 1290-1295. doi: 10.1101/gr.275193.120
    [6]
    SHUMATE A, WONG B, PERTEA G, et al. Improved transcriptome assembly using a hybrid of long and short reads with StringTie[J]. PLoS Computational Biology, 2022, 18(6): e1009730. doi: 10.1371/journal.pcbi.1009730
    [7]
    TRAPNELL C, HENDRICKSON D G, SAUVAGEAU M, et al. Differential analysis of gene regulation at transcript resolution with RNA-seq[J]. Nature Biotechnology, 2013, 31(1): 46-53. doi: 10.1038/nbt.2450
    [8]
    SHERMAN B T, HAO M, QIU J, et al. DAVID: A web server for functional enrichment analysis and functional annotation of gene lists (2021 update)[J]. Nucleic Acids Research, 2022, 50(W1): W216-W221. doi: 10.1093/nar/gkac194
    [9]
    SZKLARCZYK D, KIRSCH R, KOUTROULI M, et al. The STRING database in 2023: Protein-protein association networks and functional enrichment analyses for any sequenced genome of interest[J]. Nucleic Acids Research, 2023, 51(D1): D638-D646. doi: 10.1093/nar/gkac1000
    [10]
    SHANNON P, MARKIEL A, OZIER O, et al. Cytoscape: A software environment for integrated models of biomolecular interaction networks[J]. Genome Research, 2003, 13(11): 2498-2504. doi: 10.1101/gr.1239303
    [11]
    ROSSMANN M P, DUBOIS S M, AGARWAL S, et al. Mitochondrial function in development and disease[J]. Disease Models & Mechanisms, 2021, 14(6): dmm048912.
    [12]
    MOR D E, SOHRABI S, KALETSKY R, et al. Metformin rescues Parkinson's disease phenotypes caused by hyperactive mitochondria[J]. Proceedings of the National Academy of Sciences of the United States of America, 2020, 117(42): 26438-26447.
    [13]
    AWASTHI S, HINDLE A, SAWANT N A, et al. RALBP1 in oxidative stress and mitochondrial dysfunction in Alzheimer’s disease[J]. Cells, 2021, 10(11): 3113. doi: 10.3390/cells10113113
    [14]
    ALLEN J, CARUNCHO H J, KALYNCHUK L E. Severe life stress, mitochondrial dysfunction, and depressive behavior: A pathophysiological and therapeutic perspective[J]. Mitochondrion, 2021, 56: 111-117. doi: 10.1016/j.mito.2020.11.010
    [15]
    鲜盼盼. 硫化氢代谢异常在孤独症社交障碍中的作用及机制研究 [D]. 西安: 中国人民解放军空军军医大学, 2023.
    [16]
    涂静怡, 王世成, 申长庆, 等. 线粒体功能障碍对认知的影响[J]. 中国细胞生物学学报, 2024, 46(5): 1054-1063.
    [17]
    陈海霞, 马欣旭, 王艺霖, 等. 线粒体功能障碍与抑郁症发病机制的研究进展[J]. 神经解剖学杂志, 2023, 39(4): 476-480.
    [18]
    HOLLIS F, VAN DER KOOIJ M A, ZANOLETTI O, et al. Mitochondrial function in the brain links anxiety with social subordination[J]. Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(50): 15486-15491.
    [19]
    TRANIELLO J F, LINKSVAYER T A, COTO Z N. Social complexity and brain evolution: Insights from ant neuroarchitecture and genomics[J]. Current Opinion in Insect Science, 2022, 53: 100962. doi: 10.1016/j.cois.2022.100962
    [20]
    FAN Y, GAO J, LI Y, et al. The variants at APOA1 and APOA4 contribute to the susceptibility of schizophrenia with inhibiting mRNA expression in peripheral blood leukocytes[J]. Frontiers in Molecular Biosciences, 2021, 8: 785445. doi: 10.3389/fmolb.2021.785445
    [21]
    GUO Q W, SI Y J, SHEN Y L, et al. Depression augments plasma APOA4 without changes of plasma lipids and glucose in female adolescents carrying G allele of APOA4 rs5104[J]. Journal of Molecular Neuroscience, 2021, 71(10): 2060-2070. doi: 10.1007/s12031-020-01766-7
    [22]
    蒲阳, 母其文, 郭志伟, 等. 老年患者阿尔兹海默病风险预测模型的建立和验证[J]. 神经损伤与功能重建, 2024, 19(7): 392-396.

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