Kirtypal Singh¹, CS Mukhopadhyay²*, Simarjeet Kaur³ and JS Arora⁴

¹Ph.D. Scholar, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana
²Senior Scientist, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana
³Simarjeet Kaur, Head and Senior Geneticist, Department of Animal Genetics and Breeding, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana
⁴Scientist, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana

*Corresponding Author: CS Mukhopadhyay, Senior Scientist, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University Ludhiana.

Received: August 19, 2022; Published: August 29, 2022

Abstract

Single nucleotide polymorphism (SNP) markers are nowadays used as potential markers for parentage determination in bovines. Five trios of each of the species, namely, Bubalus bubalis (Indian water buffalo) and Bos taurus (Holstein Friesian crosses) were selected for the study. Parentage conformity of trios (Probability of Paternity = 99.99%) with six fluorescently labelled microsatellite loci was done. Single nucleotide polymorphism-based parentage detection included identification of informative single nucleotide polymorphism (based on trio-wise allele comparison) followed by exclusion of Mendelian erroneous (MDE) SNPs for minimizing the errors. About 100 to 100 nucleotide long stretches of DNA, harbouring haplotypes (consisting of at least 5 SNPs) were identified PCR amplification followed by Sanger sequencing for validation of SNP-variations in new sets of trios. The principal component analysis (PCA) based on the Minor allele frequency (MAF) distribution was analysed. Principal component analysis have narrowed down the SNP-data to figure out the most informative SNPs. We could identify 51 and 1857 most informative SNPs for buffalo and cattle, respectively, which could explain cumulative variance of up to 95.4% and 95.43% of the components, respectively. However, the validation results were not much appreciable as some of the single nucleotide polymorphism could not be detected in those amplicons. Hence, the accuracy of parentage assignment using the SNP-based approach was quite less efficient. In conclusion, it can be stated that the microsatellite-based approach for parentage determination is well standardized and efficient in accuracy of parentage assignment has compared to the SNP-based approach for parentage assignment.

Keywords: Bovines; Microsatellite; Parentage; PCA, SNPs

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Citation

Citation: CS Mukhopadhyay., et al. “Identification of Microsatellite-Based Markers and Breed-Specific Single Nucleotide Polymorphism Panels for Parentage Assignment in Bovines". Acta Scientific Veterinary Sciences 4.9 (2022): 115-128.

Copyright

Copyright: © 2022 CS Mukhopadhyay., et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.