# Transcriptomic differences in immune- and stress-related pathways associated with artificial rearing in the endangered hog deer (Axis porcinus)

## TL;DR

Artificial rearing in endangered hog deer alters immune and stress-related genes, potentially improving survival in captivity but possibly weakening early pathogen detection.

## Contribution

This study provides the first transcriptomic analysis of artificial rearing effects in endangered hog deer, revealing molecular shifts in immunity and metabolism.

## Key findings

- Artificially reared hog deer show upregulated adaptive immune pathways and downregulated innate immune and stress response genes.
- Reduced expression of nucleotide excision repair and inflammatory pathways suggests improved adaptation to captivity.
- Altered lipid and amino acid metabolism in the artificial group may reflect differences in early nutrition.

## Abstract

The hog deer (Axis porcinus), an endangered cervid species, has experienced severe population declines, making captive breeding essential for conservation. Artificial rearing has been implemented at the Shanghai Zoo, China, to improve fawn survival; however, its physiological impacts remain unclear. To elucidate the molecular consequences of different rearing modes, we conducted a comparative blood transcriptome analysis between artificially and naturally reared hog deer.

Whole-blood RNA sequencing of 10 hog deer individuals (six naturally and four artificially reared at the Shanghai Zoo) generated 84.3 Gb of high-quality data. De novo assembly produced 178,336 unigenes, with 40.2% annotated against the NCBI non-redundant database, mainly matching cervid species. Expression profiling and principal component analysis revealed clear segregation between groups. Differential expression analysis identified 3,045 genes (560 upregulated, 2,485 downregulated) in the artificial group. Functional enrichment showed upregulation of adaptive immune pathways, including antigen presentation (major histocompatibility complex class II molecules and CD74) and B cell activation (CD79/19 and transcription factor genes EBF1/SPIB), whereas innate immune and inflammatory responses—such as cytokine production (interleukin-6) and neutrophil activation (toll-like receptor 4/CD14)—were downregulated. Stress response modules, involving xeroderma pigmentosum complementation group C in the nucleotide excision repair pathway, also showed reduced expression, suggesting improved adaptation to captive conditions. In addition, pathways related to glutamine family amino acid and lipid metabolism were more active in the artificial group, potentially reflecting differences in early nutritional regimes.

Our findings reveal that artificial rearing in hog deer induces a distinct transcriptomic signature, marked by a shift from innate to adaptive immunity, reduced stress responses, and altered metabolic activity. These molecular differences may underlie improved tolerance to captivity but could also compromise early pathogen detection. This study provides novel insight into the physiological consequences of artificial rearing and offers a molecular basis to refine management practices for endangered cervid conservation and reintroduction programs.