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.