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

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.