Multi-Tissue Transcriptomic Profiles of Tarim and Tianshan Red Deer Under Common Conditions

We profiled 132 RNA-sequencing libraries representing 11 tissues from six Tarim and six Tianshan adult male red deer maintained under common feeding and management. Tissue identity dominated expression structure among 16,308 expressed genes. Across three differential-expression model specifications, 1253 robust group-associated gene–tissue pairs were identified, involving 1184 genes and concentrated in rumen and rectum. Directional enrichment returned 77 terms meeting both within-set and study-wide false-discovery thresholds. Tianshan-group rumen genes were enriched for cytoskeletal, adhesion, ion-transport and circadian annotations, whereas Tarim-group reticulum genes were enriched for cell-surface and immune-signaling annotations. Cross-tissue recurrence was uncommon and identified a small set of annotated genes and provisional loci for follow-up. Complementary whole-genome principal component analysis (PCA) separated the recorded groups across two genotype-depth filters; weighted Weir–Cockerham FST was 0.341 and 0.325. These results describe tissue-resolved expression patterns and genetic structure in the sampled cohort. Functional, taxonomic and population-wide interpretations require independent validation.