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Genetic insights into crossbred dairy cattle of Pakistan: exploring allele frequency, linkage disequilibrium, and effective population size at a genome-wide scale

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Abstract

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 r2 statistics. LD value declined as inter-marker distance increased. The average r2 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 r2 values, while higher thresholds show increased r2 values. Additionally, smaller sample sizes exhibit higher average r2 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.

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Acknowledgements

We acknowledge the Higher Education Commission, Pakistan for providing funding to the first author for her Ph.D. Studies.

Funding

This study is funded by the Pakistan Agricultural Research Council, Agricultural Linkages Programme (ALP) with Project Identification No. AS 016 titled “Development and application of genomic selection in foreign and local cattle breeds for improvement in dairy-related traits”.

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Authors and Affiliations

  1. Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, Pakistan

    Fakhar un Nisa, Muhammad Asif, Imran Amin, Shahid Mansoor & Zahid Mukhtar

  2. Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan

    Fakhar un Nisa, Muhammad Asif, Imran Amin, Shahid Mansoor & Zahid Mukhtar

  3. Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan

    Fakhar un Nisa & Haiba Kaul

  4. Animal Biosciences, International Livestock Research Institute, Nairobi, Kenya

    Raphael Mrode

  5. Animal and Veterinary Sciences, Scotland’s Rural College, Edinburgh, UK

    Raphael Mrode

  6. International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan

    Shahid Mansoor

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  1. Fakhar un Nisa
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  2. Haiba Kaul
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  3. Muhammad Asif
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  4. Imran Amin
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Contributions

Conceptualization: FUN, RM. Data curation: FUN, MA. Formal analysis: FUN, HK. Investigation: FUN. Methodology: FUN. Project administration: SM, ZM, IA. Resources: SM, IA. Software: FUN. Supervision: RM, ZM, SM. Visualization: FUN, HK. Writing-original draft: FUN. Writing-review and editing: RM, HK, ZM, MA, SM, IA.

Corresponding author

Correspondence to Zahid Mukhtar.

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The authors declare that they have no conflict of interest.

Ethical approval

To ensure the ethical and humane treatment of animals, the study described in this research paper was approved by the Research Ethics Committee of the National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan on 10-06-2020. During blood collection, a professional veterinarian was there to ensure minimal distress and harm to the animals. Before collecting any samples, the researchers met with the owners of the farm where the animals were housed to explain the purpose of the study and obtain informed consent verbally.

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Nisa, F.u., Kaul, H., Asif, M. et al. Genetic insights into crossbred dairy cattle of Pakistan: exploring allele frequency, linkage disequilibrium, and effective population size at a genome-wide scale. Mamm Genome 34, 602–614 (2023). https://doi.org/10.1007/s00335-023-10019-y

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