Yuan Hui, Lu Jun
College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, Heilongjiang, China.
BMC Genomics. 2021 Feb 10;22(1):115. doi: 10.1186/s12864-021-07423-6.
Despite several RNA-Seq and microarray studies on differentially expressed genes (DEGs) between high- and low-abdominal fat deposition in different broiler lines, to our knowledge, gene coexpression analysis across multiple broiler lines has rarely been reported. Here, we constructed a consensus gene coexpression network focused on identifying consensus gene coexpression modules associated with abdominal fat deposition across multiple broiler lines using two public RNA-Seq datasets (GSE42980 and GSE49121).
In the consensus gene coexpression network, we identified eight consensus modules significantly correlated with abdominal fat deposition across four broiler lines using the consensus module analysis function in the weighted gene coexpression network analysis (WGCNA) package. The eight consensus modules were moderately to strongly preserved in the abdominal fat RNA-Seq dataset of another broiler line (SRP058295). Furthermore, we identified 5462 DEGs between high- and low-abdominal fat lines (FL and LL) (GSE42980) and 6904 DEGs between high- and low-growth (HG and LG) (GSE49121), including 1828 overlapping DEGs with similar expression profiles in both datasets, which were clustered into eight consensus modules. Pyruvate metabolism, fatty acid metabolism, and steroid biosynthesis were significantly enriched in the green, yellow, and medium purple 3 consensus modules. The PPAR signaling pathway and adipocytokine signaling pathway were significantly enriched in the green and purple consensus modules. Autophagy, mitophagy, and lysosome were significantly enriched in the medium purple 3 and yellow consensus modules.
Based on lipid metabolism pathways enriched in eight consensus modules and the overexpression of numerous lipogenic genes in both FL vs. LL and HG vs. LG, we hypothesize that more fatty acids, triacylglycerols (TAGs), and cholesterol might be synthesized in broilers with high abdominal fat than in broilers with low abdominal fat. According to autophagy, mitophagy, and lysosome enrichment in eight consensus modules, we inferred that autophagy might participate in broiler abdominal fat deposition. Altogether, these studies suggest eight consensus modules associated with abdominal fat deposition in broilers. Our study also provides an idea for investigating the molecular mechanism of abdominal fat deposition across multiple broiler lines.
尽管已有多项关于不同肉鸡品系腹部脂肪沉积高低差异表达基因（DEGs）的RNA测序（RNA-Seq）和微阵列研究，但据我们所知，跨多个肉鸡品系的基因共表达分析鲜有报道。在此，我们构建了一个共识基因共表达网络，利用两个公开的RNA-Seq数据集（GSE42980和GSE49121），重点识别与多个肉鸡品系腹部脂肪沉积相关的共识基因共表达模块。
在共识基因共表达网络中，我们使用加权基因共表达网络分析（WGCNA）软件包中的共识模块分析功能，识别出与四个肉鸡品系腹部脂肪沉积显著相关的八个共识模块。这八个共识模块在另一个肉鸡品系（SRP058295）的腹部脂肪RNA-Seq数据集中得到了中度到高度的保留。此外，我们在腹部脂肪沉积高低品系（FL和LL）（GSE42980）之间鉴定出5462个差异表达基因，在高生长和低生长（HG和LG）（GSE49121）之间鉴定出6904个差异表达基因，其中包括1828个在两个数据集中具有相似表达谱的重叠差异表达基因，这些基因被聚类到八个共识模块中。丙酮酸代谢、脂肪酸代谢和类固醇生物合成在绿色、黄色和中紫色3个共识模块中显著富集。过氧化物酶体增殖物激活受体（PPAR）信号通路和脂肪细胞因子信号通路在绿色和紫色共识模块中显著富集。自噬、线粒体自噬和溶酶体在中紫色3和黄色共识模块中显著富集。
基于八个共识模块中富集的脂质代谢途径以及在FL与LL和HG与LG中众多脂肪生成基因的过表达，我们推测高腹部脂肪的肉鸡比低腹部脂肪的肉鸡可能合成更多的脂肪酸、三酰甘油（TAGs）和胆固醇。根据八个共识模块中自噬、线粒体自噬和溶酶体的富集情况，我们推断自噬可能参与肉鸡腹部脂肪沉积。总之，这些研究表明了与肉鸡腹部脂肪沉积相关的八个共识模块。我们的研究还为研究多个肉鸡品系腹部脂肪沉积的分子机制提供了思路。
