Abstract
The present study aimed to explore haplotype structure, runs of homozygosity (ROH), effective population size and persistence of gametic phase among three indigenous dairy cattle breeds, viz., Sahiwal (n = 19), Tharparkar (n = 17), and Gir (n = 16) by using BovineHD single nucleotide polymorphism (SNP) genotyping assay. The filtered SNPs after quality control ranged from 44% in Sahiwal to 53% in Gir. The highest number of haplotype blocks was observed in Tharparkar (15,640) and the lowest in Sahiwal (8027) spanning 17.3% and 7.8% of genome, respectively. The average block length was found close to 26 kb which suggests that multiple recombination events fragmented the ancestral haplotypes into smaller sizes. Gir cattle had the largest number of runs of homozygosity (ROH) regions (1762) followed by Tharparkar (1528) and Sahiwal (1138). Without pedigree information, inbreeding coefficients estimated from ROH (FROH) revealed that Gir had the highest FROH (0.099) proposing more inbreeding rate in this population. Effective population size (Ne) decreased slowly over the last 60 generations and at 13 generations ago; Ne was estimated as 70 for all the three dairy breeds. The highest gametic phase correlation (r = 0.78) was observed for Sahiwal and Tharparkar breed pair suggesting formulation of multi-breed reference population for successful implementation of genomic selection among dairy breeds. The decline in effective population size among native Indian cattle breeds may help in formulating strategies for conservation and genetic improvement of native germplasm for future use.
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Data availability
The BovineHD BeadChip data on three Indian dairy cattle breeds is available with the corresponding author. The dataset can be provided to the researchers on request to the corresponding author. The data is also available with the following link: http://krishi.icar.gov.in/jspui/handle/123456789/31167.
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Acknowledgements
The authors wish to express thank to ICAR-National Dairy Research Institute, Karnal (Haryana), Divya Jyoti Jagrati Sansthan, Noormahal, Jalandhar (Punjab), and Rajasthan University of Veterinary and Animal Sciences, Bikaner (Rajasthan) for providing the biological samples. This study was also supported by ICAR-National Bureau of Animal Genetic Resources to conduct the research work and data analysis.
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We would like to acknowledge the Department of Biotechnology (DBT), Government of India, for providing funds to do the research work.
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SD: own PhD research work. AS: major guide. SPD: designed the work. AK: helped in analysis. RB: compilation and writing manuscript.
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Dash, S., Singh, A., Dixit, S.P. et al. Exploring haplotype block structure, runs of homozygosity, and effective population size among dairy cattle breeds of India. Trop Anim Health Prod 55, 129 (2023). https://doi.org/10.1007/s11250-023-03534-2
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DOI: https://doi.org/10.1007/s11250-023-03534-2