Differences in Reproductive Performance Between Shiqi and Dabao Pigeons: Insights from Multi-Omics Analysis

Background/Objectives: Shiqi and Dabao pigeons are two Chinese meat-pigeon breeds with distinct breeding backgrounds and production-related phenotypes, but whether these differences extend to ovarian physiology and molecular profiles remains unclear. This study compared ovarian physiological traits and multi-omics profiles between the breeds. Methods: Seven-month-old reproductively mature females were studied. Flock-level laying and fertilization records were obtained from 456 breeding pairs per breed and recorded every 2 days. Serum reproductive hormones were measured in 10 females per breed. Follicle numbers, atresia, and mature follicle diameter were evaluated in three females per breed. Ovarian samples from six females per breed were analyzed by paired-end RNA sequencing and untargeted LC-MS/MS metabolomics in positive- and negative-ion modes. Results: Dabao pigeons had higher serum progesterone concentrations than Shiqi pigeons (1.35 ± 0.49 vs. 0.32 ± 0.19 ng/mL, p < 0.001) and larger mature follicles (2.25 ± 0.31 vs. 1.08 ± 0.56 mm, p = 0.034), whereas follicle numbers were not significantly different. Transcriptomic analysis identified 761 DEGs (FC > 2 or < 0.5; adjusted p < 0.05), mainly involving extracellular-matrix, cholesterol-, estrogen-, PI3K-Akt-, and TGF-β-related processes. Metabolomic analysis identified five differential metabolites (VIP > 1, FC > 2 or < 0.5; adjusted p < 0.05), including three taurine-conjugated bile acids. Integrated analysis revealed exploratory gene-metabolite associations related to lipid metabolism, follicular signaling, and extracellular-matrix remodeling. Conclusions: Shiqi and Dabao pigeons differed mainly in ovarian physiological and molecular characteristics, whereas short-term flock-level reproductive records were broadly similar. Metabolomic differences were limited but concentrated in bile-acid- and lipid-related features.