Selection and implementation of single nucleotide polymorphism markers for parentage analysis in crossbred cattle population
L.R. Hu,
D. Li,
Q. Chu,
Y.C. Wang,
L. Zhou,
Y. Yu,
Y. Zhang,
S.L. Zhang,
T. Usman,
Z.Q. Xie,
S.Y. Hou,
L. Liu,
W.H. Shi
Affiliations
L.R. Hu
Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, No. 4 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
D. Li
Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, No. 4 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China; Beijing Xiangzhong Biotechnology Co. LTD, No. 1 Nongda South Road, Haidian District, Beijing 100080, PR China
Q. Chu
Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agriculture and Forestry Sciences, No. 33 Zhanghua Road, Haidian District, Beijing 100097, PR China
Y.C. Wang
Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, No. 4 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China; Corresponding author.
L. Zhou
Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, No. 4 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
Y. Yu
Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, No. 4 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
Y. Zhang
Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, No. 4 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
S.L. Zhang
Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, No. 4 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China
T. Usman
Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, National Engineering Laboratory for Animal Breeding, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, No. 4 Yuanmingyuan West Road, Haidian District, Beijing 100193, PR China; College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Turu Road, Near Sheikh Maltoon Town, Mardan 23200, Pakistan
Z.Q. Xie
Anshan Hengli Dairy Farm, Shanchengzi Village, Anshan, Liaoning 114200, PR China
S.Y. Hou
Anshan Hengli Dairy Farm, Shanchengzi Village, Anshan, Liaoning 114200, PR China
L. Liu
Beijing Dairy Cattle Center, Qinghe Road, Haidian District, Beijing 100192, PR China
W.H. Shi
Beijing Dairy Cattle Center, Qinghe Road, Haidian District, Beijing 100192, PR China
Crossbreeding is an essential way of improving herd performance. However, frequent parentage record errors appear, which results in the lower accuracy of genetic parameter estimation and genetic evaluation. This study aims to build a single nucleotide polymorphism (SNP) panel with sufficient power for parentage testing in the crossbred population of Simmental and Holstein cattle. The direct sequencing technique in PCR products of pooling DNA along with matrix-assisted laser desorption/ionization time-of-flight MS method for genotyping the individuals was applied. A panel comprising 50 highly informative SNPs for parentage analysis was developed in the crossbred population. The average minor allele frequency for SNPs was 0.43, and the cumulative probability of exclusion for single-parent and both-parent inference met 0.99797 and 0.999999, respectively. The maker-set for parentage verification was then used in a group of 81 trios with aid of the likelihood-based parentage-assignment program of Cervus software. Reconfirmation with on-farm records showed that this 50-SNP system could provide sufficient and reliable information for parentage testing with the parental errors for mother–offspring and sire–offspring being 8.6 and 18.5%, respectively. In conclusion, a set of low-cost and efficient SNPs for the paternity testing in the Simmental and Holstein crossbred population are provided.
