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Unraveling genetic admixture in the Indian crossbred cattle by different approaches using Bovine 50K BeadChip

Abstract

With the upsurge of crossbreeding in India, the admixture levels are highly unpredictable in the composite breeds. Hence, in the present study, 72 Vrindavani animals were assessed for the level of admixture from their known ancestors that are Holstein–Friesian, Jersey, Brown Swiss, and Hariana, through three different software, namely, STRUCTURE, ADMIXTURE, and frappe. The genotype data for ancestral breeds were obtained from a public repository, i.e., DRYAD. The Frieswal crossbred cattle along with ancestral breeds like Holstein–Friesian and Sahiwal were also investigated for the level of admixture with the help of the above-mentioned software. The Frieswal population was found to comprise an average of 62.49, 61.12, and 61.21% of Holstein–Friesian and 37.50, 38.88, and 38.80% of Sahiwal estimated through STRUCTURE, ADMIXTURE, and frappe, respectively. The Vrindavani population was found to consist of on average 39.5, 42.4, and 42.3% of Holstein–Friesian; 22.9, 22.3, and 21.7% of Jersey; 10.7, 10.6, and 11.9% of Brown Swiss; and 26.9, 24.7, and 24.1% of Hariana blood estimated through STRUCTURE, ADMIXTURE, and frappe, respectively. A greater degree of variation was noted in the results from STRUCTURE vs. frappe, STRUCTURE vs. ADMIXTURE than in ADMIXTURE vs. frappe. From this study, we conclude that the admixture analysis based on a single software should be validated through the use of many different approaches for better prediction of admixture levels.

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Fig. 1

Data availability

The database contents (i.e., Dryad repository: http://widde.toulouse.inra.fr/widde/widde/main.do?module=cattle) and tools are all freely available online.

Code availability

Not applicable.

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Acknowledgements

The authors wish to acknowledge the Director, ICAR-IVRI, Izatnagar, Bareilly (Uttar Pradesh), India, for providing the necessary facilities and support to carry out this work.

Funding

This study was financially supported by ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly (Uttar Pradesh), India.

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Authors

Contributions

DP: wrote the manuscript and conducted sampling.

MP: conceptualized the study, contributed to study design, and data analysis.

SC: edited the manuscript, conducted sampling, and data analysis.

HK: edited the manuscript, reviewed the manuscript and data analysis.

SSN: edited and reviewed the manuscript.

DR: edited and reviewed the manuscript.

SP: edited and reviewed the manuscript.

GGK: provided resources and feedback on the study.

TD: provided resources and feedback on the study.

BB: provided resources and feedback on the study.

Corresponding author

Correspondence to Manjit Panigrahi.

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Pal, D., Panigrahi, M., Chhotaray, S. et al. Unraveling genetic admixture in the Indian crossbred cattle by different approaches using Bovine 50K BeadChip. Trop Anim Health Prod 54, 135 (2022). https://doi.org/10.1007/s11250-022-03133-7

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  • DOI: https://doi.org/10.1007/s11250-022-03133-7

Keywords

  • Admixture
  • Crossbred cattle
  • Frieswal and Vrindavani