Detection of differentially expressed genes in bantam chickens providing insights into chicken dwarfism.

BACKGROUND: The genetic basis of dwarfism in chickens, particularly in bantam chickens, is of significant interest as it provides insights into the mechanisms that underlie body size variation and growth. To better understand how gene expression changes contribute to the reduced growth in bantam chickens, we generated RNA-seq data derived from chicken embryos of varying sizes. These embryos were sampled at two developmental stages: early (E5) and later (E13). Differentially expressed genes at each stage were identified for different chicken breeds by comparing the bantam chickens against their normal-sized counterparts. RESULTS: We detected differentially expressed genes (DEGs) involved in growth-related signaling pathways, such as FGF, COL, and BMP gene families, biological processes like myogenesis and osteogenesis, and genes previously reported as potential bantam candidates, such as RNASEH2B. Notably, DEGs associated with the bantam phenotype were detectable as early as embryonic stage E5. CONCLUSIONS: DEGs showed limited overlap across different Dutch local chicken breeds, supporting the hypothesis of genetic heterogeneity contributing to the bantam phenotype. The genes and signaling pathways identified in this study offer new insights into the molecular basis of growth reduction in chickens. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12863-025-01387-2.