Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Background: In China, the widespread crossbreeding between Simmental and Holstein is a universal way so as to better improve the comprehensive benefits, as well as decline the inbreeding coefficient. However, the wrong parentage appeared frequently in this population than others due to not only the reasons in pure breeds, but more importantly, the lack of enough attention, which caused the lower accuracy of genetic parameter estimation and genetic evaluation in breeding systems. Single nucleotide polymorphism (SNP) panel in a certain population as a powerful tool for parentage assignment has been reported in numerous studies, especially in cattle. Therefore, the aim of this study was to build an SNP panel with sufficient power for parentage testing in the crossbred population of Simmental and Holstein in China. Results: In the present study, combining direct sequencing method in polymerase chain reaction (PCR) products of deoxyribonucleic acid (DNA) pooling and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) genotyping method in individuals, a panel comprising 50 highly informative single nucleotide polymorphisms (SNPs) for parentage analysis was developed in a crossbred Chinese cattle population. The average minor allele frequency (MAF) was 0.43 and the cumulative exclusion probability for single-parent and both-parent inference met 0.99797 and 0.999999, respectively. The maker-set was then used for parentage verification in a group of 81 trios with the likelihood-based parentage-assignment program of Cervus software. Compared with on-farm records, the results showed that this 50-SNP system could provide sufficient and reliable information for parentage testing with the parental mistakes for mother-offspring and sire-offspring being 8.6% and 18.5%, respectively.Conclusion: Knowledge of these results, we provided one set of low-cost and efficient SNPs for running paternity testing in the crossbred cattle population of Simmental and Holstein in China. Keywords: Parentage analysis, Single nucleotide polymorphism (SNP), Chinese crossbred cattle