Interrogation of Differentially Expressed Genes Governing Residual Feed Intake in Chickens Using RNA-Seq

Since feed cost is a major determinant for profitability in livestock production, how to improve feed efficiency through genetic selection is an intriguing subject for breeders and producers. As a more suitable indicator assessing feed efficiency, residual feed intake (RFI) is defined as the difference between observed and expected feed intake based on maintenance and growth. In this study, we quantified duodenal transcriptional architecture of extreme RFI phenotypes in the six brown-egg dwarf hens using RNA sequencing technology. In total, we obtained 59,232,077~79,010,564 uniquely mapped reads that covered 82.90% of the current annotated genes. Among these mapped reads, 75.62% fell into annotated exons, 5.50% were located in introns, and the remaining 18.88% were assigned to intergenic regions. A differential expression analysis between the high and low RFI groups identified 26 candidate genes. Functional annotation analysis revealed that these genes belong to several specific biological functions related to digestion, endopeptidase activity and proteolysis. Some genes were also found to be involved in the glycerolipid metabolism pathway. This work suggested that these potentially functional genes could affect individual feed efficiency by regulating digestion and metabolism process of the organism. Our findings pinpointed promising candidate genes of functional relevance and would be helpful to guide future breeding strategies to improve the feed efficiency.