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

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
JournalBiochemical Genetics
Early online date25 Apr 2024
Publication statusFirst published - 25 Apr 2024

Bibliographical note

Publisher Copyright:
© The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2024.


  • Admixture
  • Crossbred dairy cattle
  • FST
  • Integrated haplotype score (iHS)
  • PCA
  • XP-EHH


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