A 50-tissue transcriptome atlas of the duck for gene network and functional analysis

Ducks are economically important in global poultry production and serve as valuable models for avian biology. However, the absence of a sex-specific, multi-tissue reference of duck gene expression has limited investigations into transcriptional regulation and complex traits. Here, we constructed a transcriptome atlas covering 50 tissues from six adult Nonghua Ma ducks (three males and three females). Poly(A) RNA-seq reads were mapped to the ZJU1.0 reference genome to quantify gene expression and construct co-expression networks, and expression patterns were summarized by clustering analyses. In total, 23,512 genes were detected, with tissues clustering according to organ systems. The network yielded 12,835 clusters, of which the 50 largest encompassed 61.5 % of all genes and represented major biological processes such as neuronal signaling, immune regulation, reproduction, and metabolism. A set of 306 hub genes captured key regulators of tissue functions. Furthermore, we identified a refined panel of 13 highly stable housekeeping genes (e.g., EEF2, RPL6, RPL24) that showed superior cross-tissue stability compared with commonly used references. The atlas also revealed organ-specific sex-biased expression and incomplete Z-linked dosage compensation in females, particularly evident in digestive and musculoskeletal tissues. This sex-resolved 50-tissue transcriptome atlas of the duck provides tissue-resolved expression profiles, functional modules, and validated normalization genes to support functional genomics, biomarker discovery, molecular breeding, and comparative avian studies.