Single-cell RNA sequencing reveals depot-specific characteristics of adipose progenitor cells in ducks

Depot-specific fat deposition influences carcass yield and meat quality in ducks. To explore regulatory mechanisms, we profiled adipogenic progenitor cells (APCs) from pectoral muscle (PM), subcutaneous (SAT), and visceral adipose tissue (VAT) using single-cell RNA sequencing. Nine major cell types were identified, with APCs being most abundant in VAT and least abundant in PM, consistent with histological findings. Transcriptomic comparisons revealed depot-specific microenvironments: PM was enriched with myogenic-related pathways, SAT with immune and inflammatory responses, and VAT with pro-adipogenic signaling. Next, APCs were regrouped into 5 subclusters. Cluster 0 (PI16^high PDGFRB^high) enriched in SAT/VAT showed activated signaling of BMP and glycolysis, indicating strong adipogenic potential. Cluster 1 (PDGFRA^high F3^high) enriched in PM was associated with Wnt signaling, which maintains APCs in a progenitor state. Cell cycle, RNA velocity, and pseudotime analyses indicated that APCs of SAT/VAT were more advanced in differentiation, while APCs of PM retained stronger proliferative capacity. Cell-cell communication analysis further revealed more active paracrine regulation within SAT/VAT, while APCs from PM showed limited signaling interactions. Key depot-specific regulators were identified, including NEGR1 (PM), CD36 (SAT), and RSPO2 (VAT), which may contribute to regulations of the adipogenic process. This study provides the first single-cell atlas of duck APCs across depots, revealing molecular heterogeneity, lineage dynamics, and niche-specific regulation. These findings advance understanding of depot-specific adipogenesis and offer targets to enhance IMF while limiting excessive SAT and VAT, thereby improving both meat quality and production efficiency.