26. Performance of bovine high density SNPs genotyping array in indigenous Pakistani cattle breeds

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Published Mar 2, 2018

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Hamid Mustafa
Department of Livestock Production, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki–Pakistan
Waqas Ahmad Khan
Department of Biotechnology, Faculty of Science, University of Sargodha, Sargodha-Pakistan
Huson J. Heather
Department of Animal Sciences, Cornell University, Ithaca, NY-USA
Zulfiqar Hussain Kuthu
Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Azad Kashmir-Pakistan
Kim EuiSoo EuiSoo
Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705-USA
Adeela Ajmal
Department of Livestock Production, University of Veterinary and Animal Sciences, Ravi Campus, Pattoki–Pakistan
Noor Ul Ain
The University of Agriculture, Peshawar-Pakistan
Tad S. Sonstegard
Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, Maryland 20705-USA

Abstract

The bovine high density SNPs genotyping array has a wide range of applications including detection of selection signatures, identification of copy number variants (CNVs), genome wide association studies, and dendrogram relationships. This array can also be used to improve the accuracy of genomic predictions for low heritable traits viz. reproductive traits. The effectiveness of this array for genomic selection mainly depends on polymorphism level. In this study, we used 136 individuals from ten different Pakistani cattle breeds, include Achi (18), Bhagnari (14), Cholistani (13), Dajal (10), Dhanni (10), Kankraj (12), Lohani (19), Red Sindhi (13), Sahiwal (14), and Tharparkar (13) using high density SNPs genotyping and this array contained approximately 777, 962 SNPs. The results of this study revealed that approximately 500, 939 SNPs were found polymorphic in these breeds. The results indicate that high density SNPs bead chip would offer an informative genotyping platform for quantitative trait loci (QTL) mapping in indigenous Pakistani cattle breeds.


Keywords: Copy number variants; Genotyping; Polymorphism; Quantitative trait loci; SNPs


http://dx.doi.org/10.19045/bspab.2018.70026

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How to Cite
MUSTAFA, Hamid et al. 26. Performance of bovine high density SNPs genotyping array in indigenous Pakistani cattle breeds. Pure and Applied Biology (PAB), [S.l.], v. 7, n. 1, p. 221-226, mar. 2018. ISSN 2304-2478. Available at: <https://mail.thepab.org/index.php/journal/article/view/381>. Date accessed: 17 mar. 2025.
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Issue
Vol 7 No 1: March-2018
Section
Research Articles

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