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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Genetic insights into crossbred dairy cattle of Pakistan: exploring allele frequency, linkage disequilibrium, and effective population size at a genome-wide scale
Mammalian Genome, Volume 34, No. 4, Year 2023
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Description
Linkage disequilibrium (LD) affects genomic studies accuracy. High-density genotyping platforms identify SNPs across animal genomes, increasing LD evaluation resolution for accurate analysis. This study aimed to evaluate the decay and magnitude of LD in a cohort of 81 crossbred dairy cattle using the GGP_HDv3_C Bead Chip. After quality control, 116,710 Single Nucleotide Polymorphisms (SNPs) across 2520.241 Mb of autosomes were retained. LD extent was assessed between autosomal SNPs within a 10 Mb range using the r 2 statistics. LD value declined as inter-marker distance increased. The average r 2 value was 0.24 for SNP pairs < 10 kb apart, decreasing to 0.13 for 50–100 kb distances. Minor allele frequency (MAF) and sample size significantly impact LD. Lower MAF thresholds result in smaller r 2 values, while higher thresholds show increased r 2 values. Additionally, smaller sample sizes exhibit higher average r 2 values, especially for larger physical distance intervals (> 50 kb) between SNP pairs. Effective population size and inbreeding coefficient were 150 and 0.028 for the present generation, indicating a decrease in genetic diversity over time. These findings imply that the utilization of high-density SNP panels and customized/breed-specific SNP panels represent a highly favorable approach for conducting genome-wide association studies (GWAS) and implementing genomic selection (GS) in the Bos indicus cattle breeds, whose genomes are still largely unexplored. Furthermore, it is imperative to devise a meticulous breeding strategy tailored to each herd, aiming to enhance desired traits while simultaneously preserving genetic diversity. © 2023, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.
Authors & Co-Authors
Kaul, Haiba
Pakistan, Lahore
University of Veterinary and Animal Sciences, Lahore
Amin, Imran J.
Pakistan, Faisalabad
National Institute for Biotechnology and Genetic Engineering Pakistan
Pakistan, Islamabad
Pakistan Institute of Engineering and Applied Sciences
Mrode, Raphael A.
Kenya, Nairobi
International Livestock Research Institute Nairobi
United Kingdom, Edinburgh
Scotland’s Rural College Sruc
Mansoor, Shahid
Pakistan, Faisalabad
National Institute for Biotechnology and Genetic Engineering Pakistan
Pakistan, Islamabad
Pakistan Institute of Engineering and Applied Sciences
Pakistan, Karachi
University of Karachi
Mukhtar, Zahid
Pakistan, Faisalabad
National Institute for Biotechnology and Genetic Engineering Pakistan
Pakistan, Islamabad
Pakistan Institute of Engineering and Applied Sciences
Statistics
Authors: 5
Affiliations: 6
Identifiers
Doi:
10.1007/s00335-023-10019-y
ISSN:
09388990
Research Areas
Genetics And Genomics
Study Design
Cross Sectional Study
Cohort Study