Consensus gene co-expression analysis across multiple intestinal tissues to identify key genes and pathways associated with abdominal fat deposition in broilers

1. Abdominal fat deposition (AFD) is regulated by multiple intestinal tissues, and changes in the function of intestinal tissues are associated with AFD. Currently, integration of transcriptomic data across multiple intestinal tissues to explore excessive AFD has rarely been reported in broilers. 2. In this study, a consensus gene co-expression network across the duodenum, jejunum, ileum and caecum of high- and low-abdominal fat broiler lines (HL and LL) was constructed using a publicly available transcriptomic data set. Combining the results of functional enrichment analyses and differential gene expression analyses, this investigated the genes and biological pathways across the four intestinal tissues that might influence AFD. 3. In one expression module, <i>NDUFA5</i>, <i>NDUFS6</i>, <i>NDUFA4</i>, <i>NDUFS4</i>, <i>ATP5H</i>, <i>ATP5J</i> and <i>ATP5C1</i> were significantly enriched in the oxidative phosphorylation pathway, with <i>GPX2</i> and <i>GSR</i> significantly enriched in the glutathione metabolism pathway. These genes were significantly downregulated in the four intestinal tissues of the HL compared to LL chickens, which may be associated with AFD by increasing intestinal permeability. 4. Lipid metabolism relevant genes were identified in other modules (<i>ALDH7A1</i>, <i>ACSBG1</i>, <i>THEM4</i> and <i>DECR1</i>), which may be linked to AFD through regulation of lipid metabolism. Interestingly, in the first module, 12 genes were significantly enriched in the proteasome pathway and significantly downregulated in the four intestinal tissues in HL birds compared to LL birds, indicating a link between the proteasome and AFD.

1. 腹部脂肪沉积（Abdominal fat deposition, AFD）受多种肠道组织调控，肠道组织功能改变与腹部脂肪沉积密切相关。目前，针对肉鸡腹部脂肪过度沉积，整合多肠道组织转录组数据开展的相关研究尚未见较多报道。
2. 本研究依托公开转录组数据集，构建了高低腹脂肉鸡品系（高腹脂系HL、低腹脂系LL）十二指肠、空肠、回肠及盲肠的共识基因共表达网络。结合功能富集分析与差异基因表达分析结果，本研究探究了可能影响腹部脂肪沉积的四种肠道组织共有的关键基因及生物学通路。
3. 在某一表达模块中，NDUFA5、NDUFS6、NDUFA4、NDUFS4、ATP5H、ATP5J及ATP5C1等基因显著富集于氧化磷酸化通路，GPX2与GSR则显著富集于谷胱甘肽代谢通路。与低腹脂系肉鸡相比，上述基因在高腹脂系肉鸡的四种肠道组织中均显著下调，其或可通过提升肠道通透性参与腹部脂肪沉积进程。
4. 其他模块中鉴定到脂代谢相关基因（ALDH7A1、ACSBG1、THEM4及DECR1），其可能通过调控脂代谢通路与腹部脂肪沉积相关联。值得注意的是，在首个表达模块中，另有12个基因显著富集于蛋白酶体通路，且在高腹脂系肉鸡的四种肠道组织中同样显著下调，提示蛋白酶体通路与腹部脂肪沉积存在潜在关联。