Integrated Transcriptomic and Metabolomic Analysis Deciphers the Molecular and Metabolic Mechanisms Underlying Growth Rate Divergence in Dezhou Donkeys.

Abstract

Dezhou donkey is a premium indigenous Chinese livestock breed with high economic value for meat, hide and medicinal uses, and growth rate is a core trait determining farming profitability. However, the molecular and metabolic mechanisms underlying divergent growth rates in this breed have not been fully characterized, with no integrated transcriptomic and metabolomic studies reported. Here, 12 age-matched healthy male Dezhou donkeys were assigned to faster-growing (n = 6) and slower-growing (n = 6) groups by average daily gain, followed by plasma transcriptome sequencing and untargeted LC-MS/MS metabolomics. We identified 480 differentially expressed genes, with the slower-growing group enriching in immune/inflammatory/apoptotic pathways, and the faster-growing group in energy metabolism and transmembrane transport. Lipids and lipid-like molecules represented the largest proportion (44.9%) of the differential metabolites; the slower-growing group was enriched in lipid peroxidation and pro-inflammatory mediators, while the faster-growing group was enriched in unsaturated fatty acids and antioxidants. Integrated analysis revealed core pathways (cAMP signaling, arachidonic acid/unsaturated fatty acid biosynthesis) and key candidate genes/metabolites. Our findings clarify that excessive lipid peroxidation and inflammatory imbalance restrict growth, while efficient energy metabolism promotes faster growth, providing theoretical support for genetic improvement and precision nutrition of Dezhou donkeys.