Residual feed intake (RFI) is a measurement of feed efficiency, and is inversely correlated with feed efficiency. The differentially expressed genes (DEGs) associated with RFI vary substantially among studies, posing great challenges in finding the RFI-related marker genes. This study attempted to resolve this issue by integrating and comparing the multiple transcriptome sequencing data associated with RFI in the cattle liver, using differential, functional enrichment, protein–protein interaction (PPI) network, weighted co-expression network (WGCNA), and gene set enrichment analyses (GSEA) to identify the candidate genes and functional enrichment pathways that are closely associated with RFI. Four candidate genes namely SHC1, GPX4, ACADL, and IGF1 were identified and validated as the marker genes for RFI. Four functional enrichment pathways, namely the fatty acid metabolism, sugar metabolism, energy metabolism, and protein ubiquitination were also found to be closely related to RFI. This study identified several genes and signaling pathways with shared characteristics, which will provide new insights into the molecular mechanisms related to the regulation of feed efficiency, and provide basis for molecular markers related to feed efficiency in beef cattle.

剩余采食量 (RFI) 是衡量饲料效率的指标，与饲料效率成反比。与 RFI 相关的差异表达基因 (DEGs) 因研究而异，这对寻找 RFI 相关标记基因提出了巨大挑战。本研究试图通过整合和比较牛肝脏中与 RFI 相关的多个转录组测序数据，使用差异、功能富集、蛋白质-蛋白质相互作用 (PPI) 网络、加权共表达网络 (WGCNA) 和基因来解决这个问题。集富集分析 (GSEA) 以识别与 RFI 密切相关的候选基因和功能富集途径。四个候选基因，即SHC1、GPX4、ACADL和IGF1被鉴定和验证为 RFI 的标记基因。还发现四种功能富集途径，即脂肪酸代谢、糖代谢、能量代谢和蛋白质泛素化与 RFI 密切相关。本研究确定了几个具有共同特征的基因和信号通路，将为了解与饲料效率调节相关的分子机制提供新的见解，并为肉牛饲料效率相关的分子标记提供基础。