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Volume 17
Issue 2
10.3390/genes17020179
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Identification of Key Genes Regulating Body Weight in Qingyuan Partridge Chickens During Development using RNA-Sequence Analysis

by
Junyi Zhuang
1,†,
Weifang Yang
2,†,
Yanji Chen
1,
Shuang Liu
1,
Xucheng He
1,
Jiguang Deng
3,
Yucheng Zhang
3,
Maiqing Zheng
1,
Guiping Zhao
1,4,
Jie Wen
1 and
Huanxian Cui
1,4,*
1
State Key Laboratory of Animal Biotech Breeding, State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
2
Beijing General Station of Animal Husbandry, Beijing 100107, China
3
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
4
National Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Sanya 572024, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Genes 2026, 17(2), 179; https://doi.org/10.3390/genes17020179
Submission received: 18 December 2025 / Revised: 29 January 2026 / Accepted: 30 January 2026 / Published: 31 January 2026
(This article belongs to the Section Animal Genetics and Genomics)
Versions Notes

Abstract

Background: The Qingyuan partridge chicken is a high-quality local chicken breed in China. Its weight gain directly affects breeding efficiency. This study used RNA sequencing to analyze gene expression dynamics in the breast muscle tissue of Qingyuan partridge chickens at 1, 35, 70, and 105 days of age. Methods: This study employed RNA-sequencing, integrated with differential expression analysis, weighted gene co-expression network analysis (WGCNA), and short time-series expression miner (STEM) analysis, to systematically investigate the transcriptomic dynamics in breast muscle tissue across four developmental stages. Results: Phenotypic analysis revealed a significant increase in both body weight (BW) and breast muscle weight with age (p < 0.05). Transcriptomic analysis identified 3521 genes specifically expressed at the age of one day compared with the other 3 ages. These were significantly enriched in pathways related to ribosomal biosynthesis, cytoskeletal regulation, and cell proliferation (p < 0.05). Turquoise and black modules were identified by WGCNA, containing 1563 hub genes, which significantly correlated with BW. Integration of differentially expressed genes and STEM analysis selected 26 BW-related key genes closely associated with muscle growth, including calmodulin 2 (CALM2), heat shock protein 90 alpha family class A member 1 (HSP90AA1), and cholinergic receptor nicotinic delta subunit (CHRND). Protein–protein interaction analysis revealed two functional networks centered around these genes. Enrichment analysis of the STEM profiles indicated that upregulated genes were significantly enriched in autophagy and the ErbB, FoxO, mTOR, and insulin signaling pathways, while genes related to the ribosome, cell cycle, and PPAR signaling pathways were downregulated. Conclusions: This study identified BW-related key genes and pathways, enriching our knowledge of the functional maintenance of chicken BW.
Keywords: body weight; RNA-seq; weighted gene co-expression network analysis; key gene body weight; RNA-seq; weighted gene co-expression network analysis; key gene

Share and Cite

MDPI and ACS Style

Zhuang, J.; Yang, W.; Chen, Y.; Liu, S.; He, X.; Deng, J.; Zhang, Y.; Zheng, M.; Zhao, G.; Wen, J.; et al. Identification of Key Genes Regulating Body Weight in Qingyuan Partridge Chickens During Development using RNA-Sequence Analysis. Genes 2026, 17, 179. https://doi.org/10.3390/genes17020179

AMA Style

Zhuang J, Yang W, Chen Y, Liu S, He X, Deng J, Zhang Y, Zheng M, Zhao G, Wen J, et al. Identification of Key Genes Regulating Body Weight in Qingyuan Partridge Chickens During Development using RNA-Sequence Analysis. Genes. 2026; 17(2):179. https://doi.org/10.3390/genes17020179

Chicago/Turabian Style

Zhuang, Junyi, Weifang Yang, Yanji Chen, Shuang Liu, Xucheng He, Jiguang Deng, Yucheng Zhang, Maiqing Zheng, Guiping Zhao, Jie Wen, and et al. 2026. "Identification of Key Genes Regulating Body Weight in Qingyuan Partridge Chickens During Development using RNA-Sequence Analysis" Genes 17, no. 2: 179. https://doi.org/10.3390/genes17020179

APA Style

Zhuang, J., Yang, W., Chen, Y., Liu, S., He, X., Deng, J., Zhang, Y., Zheng, M., Zhao, G., Wen, J., & Cui, H. (2026). Identification of Key Genes Regulating Body Weight in Qingyuan Partridge Chickens During Development using RNA-Sequence Analysis. Genes, 17(2), 179. https://doi.org/10.3390/genes17020179

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