Integrated Bulk and Single-Nucleus Transcriptomics Characterizes the Developmental and Regional Specialization of...

Excessive abdominal fat deposition reduces feed efficiency and edible carcass yield in chickens, yet its developmental and regional specialization remains poorly understood. We generated 93 bulk RNA sequencing (RNA-seq) libraries from 15 fat-associated anatomical regions at embryonic day 16 (E16) and 16 regions at 2 weeks post-hatch (2w) in six Xinghua chickens. Exploratory single-nucleus RNA sequencing was additionally performed on abdominal region (AR) tissue from one individual at each stage. Repeated-measures-aware analysis identified developmental stage as the major source of transcriptomic variation, with 4556 genes expressed at higher levels at E16 and 4528 at 2w. E16-associated programs were enriched for proliferation, morphogenesis, and structural development, whereas postnatal programs were dominated by immune and stimulus-response processes. Stage-specific weighted gene co-expression network analysis (WGCNA) identified substantial regional heterogeneity. AR showed stage-dependent signatures, including higher developmental and morphogenetic programs and lower lipid-metabolic programs at E16, and higher cell-cycle-related and lower developmental and fatty-acid-metabolic programs at 2w. Single-nucleus analysis identified adipose-lineage and multiple non-adipocyte populations, and cross-omics mapping showed that AR-associated signatures were distributed across multiple cellular compartments. These results suggest stage-dependent, multicellular transcriptional specialization of chicken AR tissue.