# Genetic Analysis of the Conserved Population of Dengchuan Cattle Based on High Concordance SNP loci

## TL;DR

This study analyzes the genetic diversity of Dengchuan cattle, a rare Chinese dairy breed, to support their conservation and prevent loss of genetic variation.

## Contribution

The study identifies 61 high-concordance SNP markers for breed purity verification and provides genetic insights for conservation strategies.

## Key findings

- Dengchuan cattle maintain moderate genetic diversity but have a very low effective population size.
- 61 high-stability SNP markers were identified to assess breed purity and support conservation efforts.
- Bulls show slightly higher inbreeding levels and clearer lineage distinctions compared to females.

## Abstract

Dengchuan cattle are a rare local dairy breed from Southwest China, famous for their high milk fat content and cultural importance. Unfortunately, their numbers have declined sharply because of uncontrolled crossbreeding with foreign cattle. This study set out to investigate the genetic status of the remaining population and to provide tools for their conservation. Using a set of genetic markers called single-nucleotide polymorphisms, we examined the genetic variation of 74 animals. The results showed that the cattle still maintain a moderate level of genetic diversity, which means there is some variety left in their genes. At the same time, we found that the number of breeding animals that effectively contribute to the next generation is very low, and some family lines are over-represented. This situation may cause a loss of genetic variation in the future. Importantly, we identified 61 genetic markers that can be used to check the purity of Dengchuan cattle. These markers will help breeders to maintain the unique features of this valuable breed. Our findings highlight the urgent need to carefully manage and protect Dengchuan cattle so that they can continue to serve as an important resource for future farming and cultural heritage.

Local livestock genetic resources are crucial for sustainable agriculture and biodiversity conservation. Dengchuan cattle, a nationally protected dairy breed in China, are esteemed for their high milk fat content and cultural significance. However, they have been threatened by crossbreeding with exotic high-yielding breeds, resulting in a decline in purebred resources. In this study, we evaluated the genetic diversity and structure of a conserved population using 100K SNP microarray data from 74 individuals. After implementing strict quality control measures, 78,460 loci were retained for principal component analysis (PCA), which identified 100 SNPs most associated with PC1. After calculating high-consistency loci using PLINK, based on allelic consistency, we selected 61 high-stability markers to represent 60 individuals for further analysis. Genetic diversity parameters indicated moderate polymorphism, with an effective population size (Ne) of 2.293, observed heterozygosity (Ho) of 0.300, expected heterozygosity (He) of 0.326, and an average polymorphic information content (PIC) of 0.261. A paired t-test confirmed a highly significant difference between Ho and He (p < 0.001). Runs of homozygosity (ROH) revealed a moderate level of inbreeding (FROH = 0.0928), with bulls exhibiting slightly higher values than females. Neighbor-joining (NJ) clustering further indicated clear lineage distinctions among bulls, but lower kinship among females. Overall, Dengchuan cattle exhibit moderate genetic diversity but face risks due to a small Ne and an unbalanced family structure. Targeted breeding strategies and genetic monitoring are recommended to ensure sustainable conservation and utilization.