Transcriptome Analysis Identifies Candidate Genes and Signaling Pathways Associated With Feed Efficiency in Xiayan Chicken

Abstract

Feed efficiency is an important economic factor in poultry production, and the rate of feed efficiency is generally evaluated using residual feed intake (RFI). The molecular regulatory mechanisms of RFI remain unknown. Therefore, the objective of this study was to identify candidate genes and signaling pathways related to RFI using RNA-sequencing for low RFI (LRFI) and high RFI (HRFI) in the Xiayan chicken, a native chicken of the Guangxi province. Chickens were divided into four groups based on FE and sex: LRFI and HRFI for males and females, respectively. We identified a total of 1,015 and 742 differentially expressed genes associated with RFI in males and females, respectively. The 32 and 7 Gene Ontology (GO) enrichment terms, respectively, identified in males and females chiefly involved carbohydrate, amino acid, and energy metabolism. Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 11 and 5 significantly enriched signaling pathways, including those for nutrient metabolism, insulin signaling, and MAPK signaling, respectively. Protein–protein interaction (PPI) network analysis showed that the pathways involving CAT, ACSL1, ECI2, ABCD2, ACOX1, PCK1, HSPA2, and HSP90AA1 may have an effect on feed efficiency, and these genes are mainly involved in the biological processes of fat metabolism and heat stress. Gene set enrichment analysis indicated that the increased expression of genes in LRFI chickens was related to intestinal microvilli structure and function, and to the fat metabolism process in males. In females, the highly expressed set of genes in the LRFI group was primarily associated with nervous system and cell development. Our findings provide further insight into RFI regulation mechanisms in chickens.

Jejunal Transcriptomic Profiling for Differences in Feed Conversion Ratio in Slow-Growing Chickens

“…Their expression may facilitate intracellular fatty acid trafficking from uptake to storage or oxidation, or from lipid droplets for secretion [ 86 , 87 , 88 ]. In accordance with our results, a previous research study in duck showed that several fatty acid binding proteins were upregulated in the jejunum of a low-FCR group [ 25 ], revealing the importance of the peroxisome proliferator-activated receptor (PPAR) pathway in poultry feed efficiency [ 23 , 25 ]. The higher LBFABP expression in the low-FCR group is also consistent with the findings of Prakash et al [ 89 ], who demonstrated that LBFABP is upregulated in high-feed efficiency broiler duodenums.…”

“…Processes related to lipids and fatty acid B-oxidation are highly enriched in the chicken jejunum [ 26 ], indicating the importance of this pathway with regard specifically to jejunal absorption. Many studies have shown that intestinal fatty acid degradation- and synthesis-, and fat transport-, metabolism-, and absorption-related genes are associated with feed efficiency in poultry [ 22 , 23 , 25 ]. PLAC8, a negative regulator of apoptosis and more highly expressed in the high-FCR group, also encodes a critical upstream protein that regulates brown fat differentiation and body weight, and controls thermoregulation [ 84 ].…”

“…Many studies have been conducted on poultry feed efficiency using RNA-seq. However, most have focused on the selection on residual feed intake [ 21 , 22 , 23 , 24 ]; few data are available on FCR selection. A prior study in ducks reported that FCR selection is associated with significant gene expression variation [ 25 ].…”

“…A prior study in ducks reported that FCR selection is associated with significant gene expression variation [ 25 ]. Recent RNA-seq studies have been conducted on native chickens [ 23 , 24 ], dwarf chickens [ 21 ], divergent lines [ 26 ], and broiler lines [ 22 , 27 ]. These report that selection for a higher feed efficiency induces gene expression variation in the chicken muscle [ 22 , 24 , 27 ], duodenum [ 21 , 22 , 23 ], and jejunum [ 22 ], for which few data are available.…”

“…Recent RNA-seq studies have been conducted on native chickens [ 23 , 24 ], dwarf chickens [ 21 ], divergent lines [ 26 ], and broiler lines [ 22 , 27 ]. These report that selection for a higher feed efficiency induces gene expression variation in the chicken muscle [ 22 , 24 , 27 ], duodenum [ 21 , 22 , 23 ], and jejunum [ 22 ], for which few data are available. Juanchich et al [ 26 ] examined gene expression in the gizzard and jejunum of broiler chickens in a line divergently selected for their digestive efficiency.…”