Comparative analysis of the hypothalamus transcriptome of laying ducks with different residual feeding intake

Abstract

Feed costs account for approximately 60 to 70% of the cost of poultry farming, and feed utilization is closely related to the profitability of the poultry industry. To understand the causes of the differences in feeding in Shan Partridge ducks, we compared the hypothalamus transcriptome profiles of 2 groups of ducks using RNA-seq. The 2 groups were: 1) low-residual feed intake (LRFI) group with low feed intake but high feed efficiency, and 2) high-residual feed intake (HRFI) group with high feed intake but low feed efficiency. We found 78 DEGs were enriched in 9 differential Kyoto Encyclopedia of Genes and Genome (KEGG) pathways, including neuroactive ligand-receptor interaction, GABAergic synapse, nitrogen metabolism, cAMP signaling pathway, calcium signaling pathway, nitrogen metabolism, tyrosine metabolism, ovarian steroidogenesis, and gluconeogenesis. To further identify core genes among the 78 DEGs, we performed protein-protein interaction and coexpression network analyses. After comprehensive analysis and experimental validation, 4 core genes, namely, glucagon (GCG), cholecystokinin (CCK), gamma-aminobutyric acid type A receptor subunit delta (GABRD), and gamma-aminobutyric acid type A receptor subunit beta1 (GABRB1), were identified as potential core genes responsible for the difference in residual feeding intake between the 2 breeds. We also investigated the level of cholecystokinin (CCK), neuropeptide Y (NPY), peptide YY (PYY), ghrelin, and glucagon-like peptide1 (GLP-1) hormones in the sera of Shan Partridge ducks at different feeding levels and found that there was a difference between the 2 groups with respect to GLP-1 and NPY levels. The findings will serve as a reference for future research on the feeding efficiency of Shan Partridge ducks and assist in promoting their genetic breeding.

Keywords: RNA-seq; Shan Partridge ducks; hypothalamus; residual feed intake; serum hormone.

Figure 1

Comparison of hormone data between Shan Partridge laying ducks with different residual feed intake. Concentrations of cholecystokinin (CCK), neuropeptide Y (NPY), ghrelin, glucagon-like peptide 1 (GLP-1), and peptide YY (PYY) were compared using a T test. *P ≤ 0.05; ns means there was no different between 2 groups.

Figure 2

Correlation analysis between samples. HRFI.1 to HRFI.6 are hypothalamic samples of high-residual feed intake ducks from 1 to 6, and LRFI.1 to LRFI.6 are hypothalamic samples of low-residual feed in take ducks from 1 to 6. The abscissa and ordinate are log10 (FPKM + 1) of the samples compared with each other (A). Volcano plot of differentially expressed genes. The abscissa represents the fold change of gene expression in hypothalamic samples of high-residual feed intake compared with that of low-residual feed intake ducks. The ordinate represents the statistical significance of the difference in the amount of gene expression. The red dot indicates the significantly upregulated genes (fold change > 2, FDR < 0.05), and the blue dot indicates the significantly downregulated genes (fold change > 2, FDR < 0.05) (B).

Figure 3

GO terms and KEGG pathways enriched by DEGs. Top 30 GO terms enrichment of DEGs in the hypothalamus. Orange indicates molecular function (MF); red indicates cellular components (CC); red indicates biological processes (BP). The dark color represents upregulated gene. The light color represents downregulated gene (A). Top 30 of KEGG pathway enrichment classifications of DEGs. The X-axis represents the Rich factor, and the Y-axis represents the name of the pathway. The point size indicates the number of DEGs enriched in the pathway, and the point color corresponds to a different P value range.

Figure 4

Map of protein-protein interaction (PPI) networks in hypothalamus. Nodes represent proteins. The node size represents the interaction between the node and other nodes, the more relationships, the larger the node. The gradient color of the nodes represents genes’ fold change. The green dot indicates a negative fold change. The red dot indicates a positive fold change. Edges represent protein-protein associations. The relationship between the 2 proteins is expressed through the thickness of the line; the thicker the line, the closer the relationship (A). Hub genes and expression profiles of PPI network. Degree is used as the evaluation criterion, and the darker the color of the node, the higher its Degree score (B). Map of KEGG and its genes’ network. Round node represents gene, the diamond node represents the KEGG pathway. The gradient color of the nodes represents genes’ fold change. The green dot indicates a negative fold change. The yellow dot indicates a positive fold change. Edges represent gene-KEGG pathway associations. The relationship between gene and KEGG pathway is expressed through the thickness of the line; the thicker the line, the closer the relationship (C).

Figure 5

Validation of differentially expressed genes (DEGs) in hypothalamus from HRFI and LRFI ducks. X-axis represents 7 selected genes associated with food intake for qRT-PCR assays and Y-axis represents the log2 (fold change) derived from RNA-Seq and qRT-PCR analysis. FC = fold change (LRFI/HRFI). *P ≤ 0.05; ns means there was no different between 2 groups.