Transcriptomic Analysis of Gene Expression Patterns in the Cecal Tissue of Liangshan Yanying Chickens and Arbor Acres (AA) Chickens Before 28 Days of Age

To dissect the molecular mechanisms underlying chicken cecal development, this study used Liangshan Yanying chickens (a local slow-growing breed) and Arbor Acres (AA) chickens (a fast-growing breed) as experimental models. Cecal tissues were collected from healthy chickens at 1, 14, and 28 days of age (<i>n</i> = 10 per breed per day of age) to measure cecal length and perform transcriptome sequencing. Through the screening of differentially expressed genes (DEGs), functional enrichment analysis, construction of protein-protein interaction (PPI) networks, and qRT-PCR validation, temporal changes in cecal development between the two breeds were systematically compared. Results showed that cecal length of both breeds increased significantly with age (<i>p</i> < 0.05), with significant differences between breeds. A total of 18 high-quality samples were obtained from transcriptome analysis (Q30 ≥ 93%), with a mapping efficiency of 86.2-90.5%. The number of DEGs was highest between 1 and 28 days of age (1844 DEGs in Liangshan Yanying chickens and 1747 DEGs in AA chickens), and the number of inter-breed DEGs reached 2133 at 28 days of age. A total of 70 DEGs with consistent expression trends were identified (22 upregulated and 48 downregulated), which were enriched in Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways such as "B cell activation", "peptide transport", and "bile acid metabolism". qRT-PCR validation indicated that the expression trends of genes (e.g., CD79B, IRF4) were highly consistent with sequencing results (R² = 0.91). PPI network analysis suggested that SLC15A1, ACE, and ENPEP were key hub genes, forming a "transport-metabolism" synergistic module. This study reveals the temporal dynamics of chicken cecal development and the molecular basis of inter-breed differences, providing a theoretical foundation for broiler genetic improvement.