International Journal of Molecular Zoology, 2025, Vol.15, No.1, 10-19 http://animalscipublisher.com/index.php/ijmz 10 Research Report Open Access Transcriptomic and Metabolomic Analysis of Feed Efficiency in Chickens Xinghao Li, Jia Xuan Institute of Life Sciences, Jiyang Colloge of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding author: jia.xuan@jicat.org International Journal of Molecular Zoology, 2025, Vol.15, No.1 doi: 10.5376/ijmz.2025.15.0002 Received: 10 Dec., 2024 Accepted: 14 Jan., 2025 Published: 24 Jan., 2025 Copyright © 2025 Li and Xuan, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Li X.H., and Xuan J., 2025, Transcriptomic and metabolomic analysis of feed efficiency in chickens, International Journal of Molecular Zoology, 15(1): 10-19 (doi: 10.5376/ijmz.2025.15.0002) Abstract Feed efficiency is an important trait in poultry breeding and farming. It is related to the utilization of resources and can also help farmers reduce costs. This study summarizes the application of transcriptomics and metabolomics in the research of chicken feed efficiency in recent years, and introduces the methods of multi-omics integration. These methods can help identify candidate genes and screen molecular markers, which are of great reference value for improving the feed conversion rate of poultry in the future, conducting molecular breeding and nutritional regulation. The results show that feed efficiency is influenced by many factors. In high-efficiency and low-efficiency chickens, the gene expression and metabolic products in the liver and intestines are different. Changes in fat and sugar metabolism, as well as the immune system, may be important ways to affect feed efficiency. This study aims to provide a reference framework for molecular improvement and nutritional intervention to enhance the conversion efficiency of poultry feed in the future. Keywords Feed efficiency; Transcriptomics; Metabolomics; Non-coding RNA; Multi-omics integration 1 Introduction Feed efficiency (FE) is a crucial trait in poultry production, which directly affects the profit of breeding. Because in some chicken breeds, feed costs can account for more than 70% of the total cost (Patience et al., 2015; Ye et al., 2024). Improving feed efficiency not only makes breeding more profitable, but also reduces the waste of resources and the discharge of manure, and is more environmentally friendly. Whether it is large-scale commercial breeding or small-scale breeding, improving feed efficiency has always been an important goal in breeding (Yi et al., 2015; Sinpru et al., 2021; Ruban and Danshyn, 2024). The genetic structure of feed efficiency is complex and the heritability is moderate. It is relatively difficult to improve this trait by traditional methods (Xiao et al., 2021; Ye et al., 2024). Feed efficiency is affected by many physiological processes, such as metabolism and immune response, etc. These processes involve many genes and interact with environmental factors, making the situation rather complex (Yang et al., 2020; Sinpru et al., 2021). Yi et al. (2015) and Ye et al. (2024) found that traditional breeding methods had low accuracy in discovering and utilizing these specific genes related to feed efficiency, which also slowed down the speed of genetic improvement. This study explored how the feed efficiency of chickens is regulated by genes through the integration of transcriptomics and metabolomics analysis, expounded the gene expression and metabolic pathways of high-efficiency and low-efficiency chickens, identified some key genes, regulatory RNAs, and important metabolic processes related to high feed efficiency. This study aims to establish a relatively complete molecular framework to facilitate more precise breeding plans in the future and also promote the genetic improvement of poultry feed efficiency. 2 Feed Efficiency Traits and Their Biological Complexity 2.1 Definitions and measurement approaches Poultry feed efficiency (FE) is mainly measured by two indicators: feed conversion rate (FCR) and residual feed intake (RFI). FCR refers to how much feed a chicken needs to consume for each additional kilogram of body
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