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Assessment of Genomic Diversity and Selective Pressures in Crossbred Dairy Cattle of Pakistan

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Abstract

Improving the low productivity levels of native cattle breeds in smallholder farming systems is a pressing concern in Pakistan. Crossbreeding high milk-yielding holstein friesian (HF) breed with the adaptability and heat tolerance of Sahiwal cattle has resulted in offspring that are well-suited to local conditions and exhibit improved milk yield. The exploration of how desirable traits in crossbred dairy cattle are selected has not yet been investigated. This study aims to provide the first overview of the selective pressures on the genome of crossbred dairy cattle in Pakistan. A total of eighty-one crossbred, thirty-two HF and twenty-four Sahiwal cattle were genotyped, and additional SNP genotype data for HF and Sahiwal were collected from a public database to equate the sample size in each group. Within-breed selection signatures in crossbreds were investigated using the integrated haplotype score. Crossbreds were also compared to each of their parental breeds to discover between-population signatures of selection using two approaches: cross-population extended haplotype homozygosity and fixation index. We identified several overlapping genes associated with production, immunity, and adaptation traits, including U6, TMEM41B, B4GALT7, 5S_rRNA, RBM27, POU4F3, NSD1, PRELID1, RGS14, SLC34A1, TMED9, B4GALT7, OR2AK3, OR2T16, OR2T60, OR2L3, and CTNNA1. Our results suggest that regions responsible for milk traits have generally experienced stronger selective pressure than others.

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All relevant data are within the paper and its supplementary data files.

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Acknowledgements

The authors express their gratitude to Army Farm, Renalakhurd, for their assistance during sample collection, and Dr. Akansha Singh from India, for her assistance during analysis. Additionally, they acknowledge the Higher Education Commission (HEC) for providing funding to the first author’s PhD studies

Funding

The current study was supported by Pakistan Agricultural Research Council, Agricultural Linkages Programme (ALP), Project#AS 016 and initiated by National Institute for Biotechnology and Genetic Engineering (NIBGE).

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Authors and Affiliations

  1. Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C), Faisalabad, 38000, Pakistan

    Fakhar un Nisa, Rubab Zahra Naqvi, Fazeela Arshad, Iram Ilyas, Muhammad Asif, Imran Amin, Shahid Mansoor & Zahid Mukhtar

  2. Pakistan Institute of Engineering & Applied Sciences (PIEAS), Nilore, Islamabad, 45650, Pakistan

    Fakhar un Nisa, Rubab Zahra Naqvi, Fazeela Arshad, Iram Ilyas, Muhammad Asif, Imran Amin, Shahid Mansoor & Zahid Mukhtar

  3. Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, 54000, Pakistan

    Fakhar un Nisa

  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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Conceptualization: Fakhar un Nisa, Raphael Mrode. Funding acquisition: Shahid Mansoor, Muhammad Asif, Imran Amin. Data curation: Fakhar Un Nisa, Muhammad Asif, Fazeela Arshad. Methodology: Fakhar un Nisa, Iram Ilyas. Formal Analysis: Fakhar un Nisa, Rubab Zahra Naqvi. Project administration: Shahid Mansoor, Raphael Mrode, Zahid Mukhtar. Manuscript Initial drafting: Fakhar un Nisa, Manuscript review & editing: Zahid Mukhtar, Raphael Mrode, Shahid Mansoor, Imran Amin.

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Correspondence to Zahid Mukhtar.

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The ethical review and approval of the animal study was conducted by the Institutional Animal Ethics Committee at the National Institute for Biotechnology and Genetic Engineering College, PIEAS, Faisalabad Pakistan.

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Nisa, F.u., Naqvi, R.Z., Arshad, F. et al. Assessment of Genomic Diversity and Selective Pressures in Crossbred Dairy Cattle of Pakistan. Biochem Genet (2024). https://doi.org/10.1007/s10528-024-10809-2

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