Regulatory Networks for Feedlot Feed Efficiency in Angus Cattle Using Multiple Tissue Transcriptomics

Beef feed efficiency is a complex trait involving many processes which combine to result in less feed consumed for a given body size and rate of gain. To better understand these processes, we performed RNAseq on five tissues related to metabolism and growth (skeletal muscle, liver, visceral adipose, pituitary, and duodenum) in eight feedlot-finished, steer progeny each of two Angus bulls with divergent genomic predictions for feed efficiency. Gene co-expression networks were created after capturing differentially expressed (DE) genes, tissue specific (TS) genes, known transcription factors, and genes harboring significant SNPs according to an independent GWAS for beef feed efficiency. Of 17,183 expressed genes, 1,026 TS and 633 DE genes were identified. Skeletal muscle had the highest relative upregulation (110 of 140 DE genes). Comparing transcriptomics data with transcription factors and GWAS genes, 15 transcription factors and 56 genes harboring a GWAS SNP were also either DE or TS. Overall, this combined omics approach revealed 2,318 genes integral to beef feed efficiency. The feed efficiency network contained 115,058 connections, of which 92.3% were between genes with highest relative expression in the same tissue and 19.9% were between genes derived from different sources (transcriptomics, transcription factors, or GWAS). These results enhance our understanding of beef feed efficiency in the context of key tissues.