# Genomic Insights into Genetic Diversity and Adaptation of Nanyang Cattle: Implications for Conservation and Breeding

## TL;DR

This study explores the genetic diversity of Nanyang cattle, showing that free-ranging populations retain more natural variation and adaptation genes compared to those in conservation programs.

## Contribution

The study identifies 170 genes linked to environmental adaptation and highlights the importance of balancing conservation with breeding for productivity.

## Key findings

- Free-ranging Nanyang cattle preserve more natural genetic variation and genes related to disease resistance and adaptation.
- 170 positively selected genes were identified, including PLCB4, which may play a role in environmental adaptation through immune and synaptic pathways.
- Conservation populations show reduced diversity in neuroplasticity-related genes due to artificial selection.

## Abstract

Nanyang cattle are one of China’s most valuable local breeds, known for their strength, calm temperament, and ability to survive in harsh environments. Yet, like many traditional animals, they face threats from modern farming practices that can reduce genetic diversity, meaning the range of traits passed from one generation to the next. In this study, we compared two groups of Nanyang cattle: one maintained in an official conservation program and another living freely in mountain regions. We found that both groups share the same origins, but the free-ranging cattle preserved more natural variation and genes linked to disease resistance and adaptation, while the conservation group showed stronger effects of human selection for traits such as growth. Notably, 170 genes were identified as playing important roles in environmental adaptation. These results show that conserving Nanyang cattle requires a careful balance between improving productivity and preserving natural resilience. Protecting the genetic resources of this breed will not only help today’s farmers but also safeguard future food security and ensure the sustainability of livestock farming.

The conservation of agricultural animal resources holds significant importance for addressing future breeding demands and promoting sustainable utilization of regional livestock genetic resources. As one of China’s five major fine cattle breeds, Nanyang cattle exhibit notable characteristics, including strong adaptability and a docile temperament. Through whole-genome comparative analysis of the Nanyang cattle core conservation population and free-ranging populations in mountainous areas, this study systematically investigated the genetic diversity, population structure, and adaptive evolutionary mechanisms of this indigenous Chinese cattle breed. Population structure analysis revealed that both groups belong to a single genetic lineage of Nanyang cattle without significant genetic differentiation; however, the free-ranging population demonstrated a slower linkage disequilibrium decay rate. Combined FST and θπ ratio analyses identified 170 positively selected genes, with KEGG enrichment highlighting glutamatergic synapse and African trypanosomiasis immune pathways. PLCB4, as a shared gene across both pathways, may exert pleiotropic functions in environmental adaptation. The core conservation population likely exhibits reduced diversity in neuroplasticity-related genes under artificial selection, whereas the free-ranging population retained more genes associated with environmental adaptation and immune response. These findings provide genomic evidence for formulating differentiated conservation strategies for Nanyang cattle, necessitating balanced co-optimization of production trait breeding and natural adaptability preservation.