# Whole Genome Insights into Genetic Diversity, Introgression, and Adaptation of Hunan Cattle

## TL;DR

This study explores the genetic diversity and adaptation of Hunan cattle using whole-genome data from 110 individuals across four regions.

## Contribution

The study identifies unique genetic traits and introgression patterns in Hunan cattle, offering insights for breeding and conservation.

## Key findings

- Hunan cattle show mixed taurine and indicine ancestry with high genetic diversity.
- Candidate genes like SLC5A2 are linked to environmental adaptation and homeostasis.
- Introgression from wild cattle and regional hybridization patterns were detected.

## Abstract

This study focused on the population structure and genetic characteristics of Hunan cattle using whole genomes of 110 individuals from four regions in Hunan. The results indicated that Hunan cattle have a mixed ancestry of taurine and indicine cattle, with high genetic diversity. Several candidate genes under selection associated with desirable traits were identified. Additionally, the study clarified the introgression of wild cattle into domestic Hunan cattle and highlights functionally relevant introgressed regions. These findings suggested that Hunan cattle possess unique genetic characteristics, such as disease resistance, hot environmental adaptability, and high-quality meat; made a substantial contribution to the development of reasonable breeding strategies and resource conservation efforts of Hunan indigenous cattle; and laid a foundation for ensuring their continued contribution to the economy and cultural heritage of the region.

Hunan Province, located in Central-South China, has a hot and humid climate, which has shaped the unique characteristics of its cattle. In this study, we analyzed the genomic diversity of 110 indigenous Hunan cattle using whole-genome sequencing and found that they have a mixed ancestry of indicine and taurine. By grouping the cattle based on their collection regions (western, central, southeastern, and southern Hunan), we used an unsupervised three-component Gaussian model to classify the runs of homozygosity (ROH) and calculated the genomic inbreeding coefficient based on runs of homozygosity (FROH) to assess inbreeding levels. The results showed that western Hunan cattle had the highest level of hybridization, while southern Hunan cattle had the lowest. Through selective sweep analysis, we identified candidate genes and pathways related to environmental adaptation and homeostasis. Notably, the SLC5A2 gene showed strong selection signals across all four regions and exhibited a distinct haplotype compared to other referenced cattle breeds. Additionally, we detected introgression from wild species into Hunan domestic cattle and analyzed their Y-chromosome haplotypes.