Transcriptome analysis reveals key genes and signalling pathways related to residual feed intake in meat-type ducks

Abstract

The feed utilisation rate is a key factor that affects the economic benefits of meat-type duck breeding. In recent years, residual feed intake (RFI) has been routinely used in poultry breeding as an index for evaluating feed utilisation. However, the genetic mechanism underlying RFI in meat-type ducks remains poorly understood. In the present study, 1 000 meat-type ducks with similar BW were randomly selected to measure BW gain and feed intake from 21 to 42 d of age to assess RFI. Six high- and six low-RFI meat-type ducks were randomly selected for a transcriptome survey of livers. Protein-protein interaction (PPI) network and gene set enrichment (GSEA) analyses were used to elucidate the molecular basis of RFI. We identified 1 297 differentially expressed genes (DEGs) in the LRFI group, of which 686 and 611 were markedly up- and downregulated, respectively. Functional annotation showed that DEGs were mainly enriched in gene ontology terms related to the regulation of biosynthetic and metabolic processes. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed significant enrichment of insulin signalling and multiple pathways related to energy metabolism. Furthermore, the PPI network analysis revealed that PRKACB, PRKAR2A, FYN, PTK2, ITGB1, ESR1, and PIK3CB were primarily related to the biological processes of lipid metabolism, glucose transport, and immunological stress and may affect RFI. Moreover, the GSEA suggested that upregulated genes in the LRFI group were associated with immune, lipid transport, and insulin signalling. ACLY and SLC50A1 were the most markedly upregulated and downregulated DEGs, respectively. In the PPI network, PRKACB, PRKAR2A, and FYN were identified as pivot genes. The aforementioned DEGs were mainly involved in lipid and glucose metabolism and inflammatory response, consistent with the KEGG and GSEA results. Therefore, these results revealed PRKACB, PRKAR2A, and FYN as potentially key genes for improving feed efficiency traits in meat-type ducks. Our results provide insights into the biological basis of RFI in meat-type ducks and will be useful for the selection of meat-type ducks with a greater feed efficiency phenotype in future breeding programmes.

Keywords: Enrichment analysis; Feed efficiency; Lipid metabolism; RNA-sequencing; Regulatory genes.