Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China.
Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
J Anim Sci. 2024 Jan 3;102. doi: 10.1093/jas/skae164.
Low level of drip loss (DL) is an important quality characteristic of meat with high economic value. However, the key genes and regulatory networks contributing to DL in pork remain largely unknown. To accurately identify the key genes affecting DL in muscles postmortem, 12 Duroc × (Landrace × Yorkshire) pigs with extremely high (n = 6, H group) and low (n = 6, L group) DL at both 24 and 48 h postmortem were selected for transcriptome sequencing. The analysis of differentially expressed genes and weighted gene co-expression network analysis (WGCNA) were performed to find the overlapping genes using the transcriptome data, and functional enrichment and protein-protein interaction (PPI) network analysis were conducted using the overlapping genes. Moreover, we used machine learning to identify the key genes and regulatory networks related to DL based on the interactive genes of the PPI network. Finally, nine potential key genes (IRS1, ESR1, HSPA6, INSR, SPOP, MSTN, LGALS4, MYLK2, and FRMD4B) mainly associated with the MAPK signaling pathway, the insulin signaling pathway, and the calcium signaling pathway were identified, and a single-gene set enrichment analysis (GSEA) was performed to further annotate the functions of these potential key genes. The GSEA results showed that these genes are mainly related to ubiquitin-mediated proteolysis and oxidative reactions. Taken together, our results indicate that the potential key genes influencing DL are mainly related to insulin signaling mediated differences in glycolysis and ubiquitin-mediated changes in muscle structure and improve the understanding of gene expression and regulation related to DL and contribute to future molecular breeding for improving pork quality.
低滴水损失（DL）水平是具有高经济价值的肉类的一个重要质量特性。然而，导致猪肉 DL 的关键基因和调控网络在很大程度上仍然未知。为了准确鉴定影响宰后肌肉 DL 的关键基因，选择了 12 头具有极高（n=6，H 组）和极低（n=6，L 组）DL 的杜洛克×（长白猪×约克夏猪）杂交猪，分别在宰后 24 和 48 小时进行转录组测序。使用转录组数据进行差异表达基因分析和加权基因共表达网络分析（WGCNA），以找到重叠基因，并使用重叠基因进行功能富集和蛋白质-蛋白质相互作用（PPI）网络分析。此外，我们使用机器学习基于 PPI 网络的交互基因来识别与 DL 相关的关键基因和调控网络。最后，鉴定出 9 个与丝裂原活化蛋白激酶信号通路、胰岛素信号通路和钙信号通路主要相关的潜在关键基因（IRS1、ESR1、HSPA6、INSR、SPOP、MSTN、LGALS4、MYLK2 和 FRMD4B），并进行单基因集富集分析（GSEA）以进一步注释这些潜在关键基因的功能。GSEA 结果表明，这些基因主要与泛素介导的蛋白水解和氧化反应有关。综上所述，我们的研究结果表明，影响 DL 的潜在关键基因主要与胰岛素信号介导的糖酵解差异和泛素介导的肌肉结构变化有关，有助于提高对与 DL 相关的基因表达和调控的理解，并为未来的分子育种改良猪肉质量提供帮助。
