Single-nucleus atlas provides insights into changes in the evolution of the pig hippocampus

The large-scale development of pig farming has introduced significant stressors that negatively affect pigs' mental health, behavior, and production efficiency. The hippocampus, crucial for cognition and stress response regulation, plays a central role in these processes. However, the regulatory mechanisms underlying hippocampal function across pig breeds with different domestication statuses and their implications for behavior and breeding strategies remain unclear.

We performed single-nucleus RNA sequencing (snRNA-seq) on hippocampal tissues from 22,342 cells across three pig breeds: Asian wild boar, Jinhua, and Duroc, representing different domestication statuses. We identified six major hippocampal cell types and annotated 108 breed-specific transcription factors, including GATA2, SPI1, and EBF1. Additionally, we characterized 83 co-expression modules and 50 significant ligand-receptor pairs, such as TGFβ, WNT, and SPP1, revealing complex intercellular communication networks. Oligodendrocyte expression patterns were conserved across all breeds. We identified 194 candidate genes linked to stress resilience, mental health, and feeding behavior, including MC4R, RYR2, PDE10A, and ABCG2. Alzheimer's disease-related gene enrichment was lower in Duroc pigs, consistent with reduced APOE expression. We also developed the Pig Hippocampus Single-cell Atlas (PHiSA, http://alphaindex.zju.edu.cn:8503/ ), an open-access database allowing breed-specific hippocampal analyses and validation of gene expression at the single-nucleus level.

This study offers insights into hippocampal function regulation in pigs, focusing on stress resilience, behavior, and productivity. It highlights conserved and breed-specific molecular features of hippocampal cell types and their roles in adaptability and mental health. By integrating single-nucleus data, the research suggests that genetic strategies could be used to improve animal welfare, stress management, and production efficiency in pig breeding programs.