Tract-wide transcriptomic and metabolomic profiling reveals gastrointestinal regionalization in Jiekarzi semi-fine wool sheep.

Jiekarzi semi-fine-wool sheep are indigenous to the Qinghai-Tibet Plateau, and may face substantial demands on digestive efficiency under low temperatures, hypoxia and seasonal forage limitation. However, the molecular organization of the gastrointestinal tract in this breed remains insufficiently characterized. Here, we profiled mucosal transcriptomes and digestive-fluid metabolomes from 10 gastrointestinal segments collected from six 12-month-old male Jiekarzi. The segments were grouped into four digestive regions: forestomach, true stomach, small intestine and large intestine. Transcriptomes analysis separated clearly by regions, with PC1 and PC2 explaining 40.82% and 15.00% of the variation, respectively. Pairwise differential expression analysis identified 4,941-9,598 differentially expressed genes, with the largest difference between the small intestine and forestomach. Region-specific enrichment indicated differences in immune processes, epithelial organization, transmembrane transport, digestion and absorption, lipid metabolism and xenobiotic associated pathways. Untargeted LC-MS detected 1,757 metabolites in positive-ion mode and 1547 metabolites in negative-ion mode. Integrated transcriptome and metabolomic patterns suggested region associated immune function, nutrient transport and metabolic specialization. These results provide a baseline molecular map of gastrointestinal regionalization for a wider area of the tract, and a reference resource for future research on digestive physiology, nutrient utilization and environmental resilience in plateau-adapted ruminants.