International Journal of Molecular Zoology, 2025, Vol.15, No.1, 10-19 http://animalscipublisher.com/index.php/ijmz 16 the same diet and environment. Some genes are concentrated in mitochondrial function and energy metabolism pathways, while others show stronger immune activation, indicating that genetic background and environmental exposure jointly affect the long-term adaptability of feed efficiency (FE) through epigenetics. As a result of the combined effects of genetics and diet, the gut microbiota is also involved in the regulation of FE. Some specific microbial groups are closely related to the improvement of nutrient absorption and metabolic efficiency. 8 Case Study: Integrated Transcriptomic and Metabolomic Analysis of Chickens with High and Low Feed Efficiency 8.1 Experimental design and individual selection strategy In this case study, two indicators, namely residual feed intake (RFI) and feed-to-meat ratio (FCR), were used to conduct phenotypic identification of feed efficiency (FE) for the chicken flock. On this basis, the chickens with the most extreme performance were selected. In the experiment, the researchers classified those with the lowest RFI or FCR as the high-efficiency group and those with the highest as the low-efficiency group. For example, from over 1 000 chickens, the 5 with the lowest RFI and the 5 with the highest RFI were selected for in-depth analysis. Some studies also grouped chickens based on high and low FCR, or specifically selected high/low RFI strains for tissue sampling and subsequent omics analysis (Yang et al., 2020; Sinpru et al., 2021; Xiao et al., 2021). 8.2 Key transcriptomic findings: differentially expressed genes closely related to feed efficiency Sinpru et al. (2021) and Wang et al. (2022) found significant differences in the expression of many genes between the high-efficiency group and the low-efficiency group of chickens in the transcriptome analysis of multiple tissues such as liver, muscle, intestine and fat. These differentially expressed genes (DEGs) are mainly concentrated in pathways such as energy metabolism, mitochondrial function, fat metabolism, carbohydrate metabolism, immune response and oxidative phosphorylation. Some key genes, including ND2, ND4, CYTB, RAC2, VCAM1, CTSS, TLR4, CAT, ACSL1, ECI2, ABCD2, ACOX1 and PCK1, are involved in ATP synthesis, reactive oxygen species control and fat metabolism (Yang et al., 2020; Xiao et al., 2021). Karimi et al. (2021) and Yuan et al. (2024) found that long non-coding RNAs (lncRNA) and circular RNAs (circRNA) are also involved in the regulation of FE and play significant roles in fat metabolism and energy balance. 8.3 Key metabolomic findings: differential metabolites and their functional significance Previous studies have found that there are significant differences between high-efficiency chickens and low-efficiency chickens in fat metabolism, carbohydrate metabolism, and metabolites related to the nitrogen cycle. The purine recycling pathway of high-efficiency chickens is more active. They can synthesize nucleotides with less energy, promote protein retention and reduce nitrogen excretion (Aggrey et al., 2014; Wang et al., 2022). These metabolic differences are closely related to the improvement of energy utilization efficiency, the reduction of fat, and the enhancement of nutrient absorption and assimilation capacity. 8.4 Multi-omics integration and practical implications The combination of transcriptome and metabolome data reveals the molecular regulatory mechanism of chicken feed efficiency. A large number of studies have found that pathways such as mitochondrial energy production, fat and carbohydrate metabolism, immune regulation, and nitrogen recovery work together in high-FE chickens, thereby improving feed efficiency (Yang et al., 2020; Sinpru et al., 2021; Xiao et al., 2021; Wang et al., 2022), these findings also provide references for breeding. The candidate genes, lncRNA and circRNA screened out through multi-omics can be used as molecular markers to help precisely select and breed chicken flocks with high feed efficiency, reduce breeding costs and improve the sustainability of the poultry industry. 9 Current Challenges and Future Opportunities 9.1 Biological and technical constraints Biologically speaking, FE is related to multiple tissues, various metabolic pathways, and complex gene regulatory networks, including lncRNA, circRNA, and tissue-specific expression patterns, which have not been fully clarified at present (Karimi et al., 2021; Xiao et al., 2021; Yuan et al., 2024). Technically, the performance varies
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