Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
College of Life Science, Luoyang Normal University, Jiqing Road, 471934 Luoyang, PR China.
Gene. 2018 Oct 5;673:211-216. doi: 10.1016/j.gene.2018.06.054. Epub 2018 Jun 19.
Incorrect paternity assignment in cattle can significantly influence the accuracy of genetic evaluation. Recent advances in high-throughput technology have facilitated the identification of single nucleotide polymorphism (SNP) markers and their applications for filiation and individual identification. We genotyped 1074 bulls from a reference population of Chinese Simmental cattle for genomic selection using a BovineSNP770K BeadChip. Among them, a total of 136 bulls were randomly selected to design a suitable low-density SNP panel for paternity testing in Simmental cattle. Our results showed that 50 SNPs were determined to be the most informative markers in parental testing, with an accuracy of 99.89% for CPE (cumulative probability of exclusion) in the unknown female parent case. The 50 highly informative SNP markers were distributed across 25 chromosomes, and the mean intermarker distance per chromosome was 26.72 Mb. The average minor allele frequency (MAF), expected heterozygosity (HE), and polymorphic information content (PIC) values were 0.3748, 0.4998, and 0.4818, respectively. Finally, the 50 identified SNPs were used to estimate paternity for the remaining 938 of 1074 bulls from 23 farms. Our results revealed that 76.75% of the 938 bulls were assigned parentage to the pedigree sires with 95% confidence, and the rate of pedigree record mistakes ranged from 9.52%-39.29% in different herds. Our study is the first attempt to provide valuable insights into the extraction of informative markers through the application of high-density SNP chips for paternity testing in Chinese Simmental cattle.
在牛中不正确的亲子关系鉴定会显著影响遗传评估的准确性。高通量技术的最新进展促进了单核苷酸多态性（SNP）标记的鉴定及其在系谱和个体识别中的应用。我们使用 BovineSNP770K BeadChip 对来自中国西门塔尔牛参考群体的 1074 头公牛进行了基因组选择的基因分型。其中，共有 136 头公牛被随机选择，以设计适用于西门塔尔牛亲子关系鉴定的低密度 SNP 面板。我们的结果表明，在未知雌性亲本的情况下，50 个 SNP 被确定为亲子关系鉴定中最具信息量的标记，累积排除概率（CPE）的准确率为 99.89%。这 50 个高度信息量的 SNP 标记分布在 25 条染色体上，每条染色体上的平均标记间距离为 26.72 Mb。平均的次要等位基因频率（MAF）、期望杂合度（HE）和多态信息含量（PIC）值分别为 0.3748、0.4998 和 0.4818。最后，用鉴定出的 50 个 SNP 来估计来自 23 个农场的 1074 头公牛中的其余 938 头公牛的亲子关系。我们的结果表明，938 头公牛中有 76.75%被分配到系谱父本，置信度为 95%，不同牛群中的系谱记录错误率从 9.52%到 39.29%不等。我们的研究首次尝试通过应用高密度 SNP 芯片提取有用的标记，为中国西门塔尔牛的亲子关系鉴定提供了有价值的见解。
