Morphological and Transcriptomic Responses of Three Intestinal Segments Following the Replacement of 50% of Dietary Soybean Meal with Walnut Cake in Finishing Large Diqing Tibetan Pigs

Alternative feed ingredients may alter intestinal structure and function. We examined jejunal, ileal, and cecal responses in Large Diqing Tibetan pigs fed a control diet or one in which walnut cake replaced 50% of soybean meal. Two pigs were sampled from each of three pens per treatment. Intestinal morphology was assessed histologically, and RNA sequencing data from 8 jejunal, 12 ileal, and 10 cecal samples retained after screening were analyzed by voom–dream, differentially expressed gene (DEG) enrichment analysis, and gene set enrichment analysis (GSEA). The 50W group showed higher villus-related indices in the jejunum and ileum and greater cecal mucosal thickness and crypt depth. The screened-sample analysis identified 103, 67, and 1979 DEGs, respectively. Pathway analyses associated jejunal responses with nutrient metabolism, ion transport, and epithelial organization; ileal responses with DNA replication, cell cycle, and epithelial renewal; and cecal responses with extracellular matrix organization and cell adhesion. Although jejunal and cecal DEG counts were sensitive to sample inclusion, principal pathway-enrichment directions were broadly maintained in full-sample and leave-one-pen-out analyses. RT-qPCR results for five selected genes showed concordant directions of expression change with the corresponding RNA-seq results.