Development and Genomic Validation of a Population-Specific SNP Panel for Parentage Verification in Chinese Holstein Cattle

Abstract

Accurate pedigree information is essential for genetic evaluation and genomic selection in dairy cattle. However, the performance of SNP-based parentage verification depends on marker informativeness, genomic distribution, and compatibility with the target population. In this study, we developed and validated a population-specific 260-SNP panel for parentage verification in Chinese Holstein cattle. The panel was selected from BovineSNP150K genotype data of 2954 Chinese Holsteins based on high marker informativeness, genotyping quality, LD-based control of marker redundancy, and genome-wide distribution. The selected SNPs had a mean minor allele frequency of 0.4981, expected heterozygosity of 0.5000, and polymorphism information content of 0.3750, with a combined probability of exclusion >0.999. Parentage verification of 867 recorded candidate parent–offspring pairs using likelihood-based and Mendelian exclusion-based approaches showed 99.54% agreement, with a Cohen’s κ of 0.981. Random SNP-subset analyses showed greater variation in pedigree concordance estimates with smaller marker sets, whereas larger subsets produced more stable estimates across replicate subsets. Independent validation using targeted-capture sequencing showed a mean SNP detection rate of 99.96% and complete genotype concordance in duplicate tests. Independent validation across six commercial dairy farms identified an overall inconsistency rate of 12.97% between recorded pedigree relationships and genotype-based parentage evidence. These results demonstrate that the population-specific 260-SNP panel provides informative and reproducible genotyping for parentage verification in Chinese Holstein cattle and offers a practical tool for pedigree quality control in dairy cattle breeding programs.