Development and Genomic Validation of a Population-Specific SNP Panel for Parentage Verification in Chinese Holstein Cattle
- 1College of Animal Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- 2Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
- 3College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
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.
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BibTeX
@article{dou2026development,
title = {{Development and Genomic Validation of a Population-Specific SNP Panel for Parentage Verification in Chinese Holstein Cattle}},
author = {Jinhuan Dou and Jingyi Gu and Ao Wang and Ziyu Luo and Hetian Huang and Xihui Sheng and Yachun Wang and Ying Yu},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = oct,
doi = {10.3390/ijms27209198},
url = {https://www.mdpi.com/1422-0067/27/20/9198},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Development and Genomic Validation of a Population-Specific SNP Panel for Parentage Verification in Chinese Holstein Cattle
AU - Jinhuan Dou
AU - Jingyi Gu
AU - Ao Wang
AU - Ziyu Luo
AU - Hetian Huang
AU - Xihui Sheng
AU - Yachun Wang
AU - Ying Yu
PY - 2026
DA - 2026/10/01
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27209198
UR - https://www.mdpi.com/1422-0067/27/20/9198
AB - 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.
SN - 1422-0067
ER -