背景:尽管对不同肉鸡系中高腹部脂肪沉积和低腹部脂肪沉积之间的差异表达基因(DEGs)进行了一些RNA-Seq和微阵列研究,根据我们的知识,多个肉鸡品系之间的基因共表达分析鲜有报道。这里,我们使用两个公共RNA-Seq数据集(GSE42980和GSE49121)构建了一个共有基因共表达网络,重点是在多个肉鸡品系中鉴定与腹部脂肪沉积相关的共有基因共表达模块.
结果:在共有基因共表达网络中,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,在4个肉鸡品系中鉴定出8个与腹部脂肪沉积显著相关的共识模块.八个共有模块在另一个肉鸡品系(SRP058295)的腹部脂肪RNA-Seq数据集中适度至强烈地保留。此外,我们确定了高和低腹部脂肪线(FL和LL)之间的5462DEG(GSE42980)和高和低生长(HG和LG)之间的6904DEG(GSE49121),包括两个数据集中具有相似表达谱的1828个重叠DEGs,它们被分成八个共识模块。丙酮酸代谢,脂肪酸代谢,类固醇生物合成在绿色中显著富集,黄色,和中等紫色3个共识模块。PPAR信号通路和脂肪细胞因子信号通路在绿色和紫色共有模块中显著富集。自噬,线粒体自噬,和溶酶体在中等紫色3和黄色共有模块中显著富集。
结论:基于富含八个共有模块的脂质代谢途径以及FL和FL中大量脂肪生成基因的过表达。LL和HGvs.LG,我们假设更多的脂肪酸,三酰基甘油(TAG),高腹脂肉鸡比低腹脂肉鸡可能合成胆固醇。根据自噬,线粒体自噬,和溶酶体在八个共识模块中的富集,推测自噬可能参与肉鸡腹部脂肪沉积。总之,这些研究表明,8个共识模块与肉鸡腹部脂肪沉积相关。我们的研究也为研究跨多个肉鸡系腹部脂肪沉积的分子机制提供了思路。
BACKGROUND: 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).
RESULTS: 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.
CONCLUSIONS: 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.