Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq

Chaoyun Yang; Liyun Han; Peng Li; Yanling Ding; Yun Zhu; Zengwen Huang; Xingang Dan; Yuangang Shi; Xiaolong Kang

doi:10.3389/fgene.2021.741878

Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq

Front Genet. 2021 Oct 5:12:741878. doi: 10.3389/fgene.2021.741878. eCollection 2021.

Authors

Chaoyun Yang¹, Liyun Han², Peng Li¹, Yanling Ding¹, Yun Zhu¹, Zengwen Huang¹, Xingang Dan¹, Yuangang Shi¹, Xiaolong Kang¹

Affiliations

¹ School of Agriculture, Ningxia University, Yinchuan, China.
² Ningxia Agriculture Reclamation Helanshan Diary Co.Ltd., Yinchuan, China.

Abstract

Residual feed intake (RFI) is an important measure of feed efficiency for agricultural animals. Factors associated with cattle RFI include physiology, dietary factors, and the environment. However, a precise genetic mechanism underlying cattle RFI variations in duodenal tissue is currently unavailable. The present study aimed to identify the key genes and functional pathways contributing to variance in cattle RFI phenotypes using RNA sequencing (RNA-seq). Six bulls with extremely high or low RFIs were selected for detecting differentially expressed genes (DEGs) by RNA-seq, followed by conducting GO, KEGG enrichment, protein-protein interaction (PPI), and co-expression network (WGCNA, n = 10) analysis. A total of 380 differentially expressed genes was obtained from high and low RFI groups, including genes related to energy metabolism (ALDOA, HADHB, INPPL1), mitochondrial function (NDUFS1, RFN4, CUL1), and feed intake behavior (CCK). Two key sub-networks and 26 key genes were detected using GO analysis of DEGs and PPI analysis, such as TPM1 and TPM2, which are involved in mitochondrial pathways and protein synthesis. Through WGCNA, a gene network was built, and genes were sorted into 27 modules, among which the blue (r = 0.72, p = 0.03) and salmon modules (r = -0.87, p = 0.002) were most closely related with RFI. DEGs and genes from the main sub-networks and closely related modules were largely involved in metabolism; oxidative phosphorylation; glucagon, ribosome, and N-glycan biosynthesis, and the MAPK and PI3K-Akt signaling pathways. Through WGCNA, five key genes, including FN1 and TPM2, associated with the biological regulation of oxidative processes and skeletal muscle development were identified. Taken together, our data suggest that the duodenum has specific biological functions in regulating feed intake. Our findings provide broad-scale perspectives for identifying potential pathways and key genes involved in the regulation of feed efficiency in beef cattle.

Keywords: beef cattle; duodenal; feed efficiency; residual feed intake; weighted gene co-expression network analysis.