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

Abstract

Combining direct sequencing method in polymerase chain reaction (PCR) products of deoxyribonucleic acid (DNA) pooling and matrix-assisted laser desorption/ionisation time of flight mass spectrometry (MALDI-TOF MS) genotyping method in individuals, a panel consisting of 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. Knowledge of these results, we provided one low-cost and efficient method of SNP assays for running paternity testing in crossbred cattle population of Simmental and Holstein in China.