Transcriptomic analysis of the intestinal tissue of male broiler chicks to identify key hub genes and miRNA associated with feed efficiency

Document Type : Research Paper

Authors

1 Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran

2 Agriculture Victoria Research Division, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, Victoria 3083, Australia

3 School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3083, Australia

Abstract

Introduction: Integrating RNA-seq and microarray data provides an advanced statistical approach to combine heterogeneous transcriptomic datasets. This approach controls technical variations and can model individual variance, thereby improving the sensitivity for identifying differentially expressed genes and enabling integrated biological pathway analysis. In the livestock and poultry breeding programs, improving feed efficiency is a key goal due to its significant economic benefits. Defined as the ratio between feed intake and weight gain or production, feed efficiency is influenced by a combination of genetic, physiological, nutritional, and environmental factors. Understanding the molecular mechanisms underlying feed efficiency variation can lead to targeted breeding strategies in selective breeding. Given the critical role of the intestine as the primary site of feed digestion and absorption, in this study, transcriptomic data from different platforms was integrated to identify genes, regulatory microRNAs, and shared biological pathways associated with feed efficiency in the duodenum of broilers. The findings support the coordinated roles of energy metabolism and gene expression regulation in intestinal feed efficiency and provide a foundation for the development of molecular markers for breeding applications.
Materials and methods: RNA-seq and microarray datasets were integrated based on the shared Ensembl ID using the BASE package in R. Batch effects across datasets were corrected using ComBat, followed by cross-platform quantile normalization. Low-expression genes were filtered using the 25th percentile threshold, and differential gene expression analysis was performed with the limma package in R. The genes with ∣logFC∣>1.5| and P<0.05 were considered significant. Gene ontology and pathway enrichment analyses were conducted using DAVID and KEGG. Protein–protein interaction networks were constructed using STRING and visualized in Cytoscape, with hub genes identified using the MCODE and CytoHubba plugins. Additionally, miRNA–mRNA regulatory networks were generated based on predictions from TargetScan and miRDB.
Results and discussion: Comparison of the gene expression profile between groups with low and high feed efficiency revealed a total of 918 significantly differentially expressed genes, including 563 downregulated and 355 upregulated genes. Pathway enrichment analysis highlighted the involvement of energy metabolism, lipid metabolism, and immune-related processes in feed efficiency. The phagosome pathway was significantly enriched, with increased expression of IL16 in the group with high feed efficiency, suggesting higher immune and inflammatory activity. In contrast, the tricarboxylic acid (TCA) cycle was among the most enriched pathways, showing higher expression levels in the group with high feed efficiency. Given the high ATP demand of the intestine for digestion, nutrient absorption, and rapid epithelial renewal, enhanced TCA cycle activity reflects more efficient energy production in the group with higher feed efficiency. Furthermore, increased expression of glutathione S-transferase family genes (GSTA2, GSTA3, GSTM1, and GSTM2) in the group with high feed efficiency indicates an improved antioxidant defense system, which may contribute to reduced oxidative stress and enhanced metabolic efficiency. The key genes involved in fatty acid metabolism (ACADL, ACSL5, EHHADH, and FABP1) were enriched in the PPAR signaling pathway, underscoring their roles in lipid oxidation and energy homeostasis. The identification of ACO1 suggests that regulation of energy metabolism extends beyond the TCA cycle and is linked to nitrogen metabolism and protein synthesis. Moreover, ribosomal protein genes, particularly RPS6, along with hub genes associated with oxidative phosphorylation (NDUFAB1, NDUFA12, NDUFA9, NDUFS6, UQCRQ, and COX7C), emphasize the major role of mitochondrial function and the mTOR–ribosome axis in enhancing ATP production efficiency and lean tissue growth. The robustness of these key genes was further supported by ROC analysis, with all identified biomarkers exhibiting AUC values greater than 0.8, highlighting their potential as molecular indicators of feed efficiency.
Conclusions: Overall, the findings of this study indicate that feed efficiency is largely influenced by the coordinated regulation of intestinal energy metabolism, mitochondrial function, and antioxidant defense systems. Higher feed efficiency was correlated with an increased activity of the TCA cycle, oxidative phosphorylation, fatty acid oxidation, and the mTOR–ribosome axis, leading to more efficient ATP production and protein synthesis. Concurrently, the upregulation of glutathione S-transferase–related genes in the group with high feed efficiency reflects improved redox balance and reduced metabolic burden, whereas higher immune-related pathway activity in the group with low feed efficiency may indicate greater energy allocation towards inflammatory processes. Collectively, these results indicate mitochondrial integrity and metabolic flexibility as key physiological mechanisms underlying feed efficiency and highlight the identified genes as promising molecular biomarkers in selective breeding and nutrition management.

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References

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Animal Production Research
Volume 15, Issue 1
March 2026
Pages 1-23

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