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Assessing accuracy of genotype imputation in the Afrikaner and Brahman cattle breeds of South Africa

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Abstract

Imputation may be used to rescue genomic data from animals that would otherwise be eliminated due to a lower than desired call rate. The aim of this study was to compare the accuracy of genotype imputation for Afrikaner, Brahman, and Brangus cattle of South Africa using within- and multiple-breed reference populations. A total of 373, 309, and 101 Afrikaner, Brahman, and Brangus cattle, respectively, were genotyped using the GeneSeek Genomic Profiler 150 K panel that contained 141,746 markers. Markers with MAF ≤ 0.02 and call rates ≤ 0.95 or that deviated from Hardy Weinberg Equilibrium frequency with a probability of ≤ 0.0001 were excluded from the data as were animals with a call rate ≤ 0.90. The remaining data included 99,086 SNPs and 360 Afrikaner, 75,291 SNPs and 288 animals Brahman, and 97,897 SNPs and 99 Brangus animals. A total of 7986, 7002, and 7000 SNP from 50 Afrikaner and Brahman and 30 Brangus cattle, respectively, were masked and then imputed using BEAGLE v3 and FImpute v2. The within-breed imputation yielded accuracies ranging from 89.9 to 96.6% for the three breeds. The multiple-breed imputation yielded corresponding accuracies from 69.21 to 88.35%. The results showed that population homogeneity and numerical representation for within and across breed strategies, respectively, are crucial components for improving imputation accuracies.

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Data availability

Data cannot be shared with the public, due to the breed society’s still participating in the Beef Genomics Program of South Africa and under the process of accumulating and preliminarily analyzing their data for their breeding program purposes.

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Acknowledgements

SM thanks the University of the Free State (UFS), the National Research Foundation (NRF), and the Technology Innovation Agency (TIA), an implementing agency of the Department of Science and Innovation for financial support. Without the financial support of the Red Meat Research and Development SA (RMRD SA) and the Beef Genomics Program (BGP), this research would not have been possible. The breed societies granting of permission to use the data is gratefully acknowledged.

Funding

This project received financial support from the Department of Science and Innovation (DSI), the Red Meat Research and Development South Africa (RMRD SA), and the South African Beef Genomics Program (BGP). We would also like to thank the southern African Brahman Breeders’ Society for their financial contribution towards the generation of genomic data.

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Authors and Affiliations

  1. Department of Animal Breeding and Genetics, Agricultural Research Council, Irene, South Africa

    S. Mdyogolo, M. D. MacNeil, M. M. Scholtz & M. L. Makgahlela

  2. Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa

    S. Mdyogolo, M. D. MacNeil, F. W. C. Neser, M. M. Scholtz & M. L. Makgahlela

  3. Delta G, Miles City, MT, USA

    M. D. MacNeil

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  1. S. Mdyogolo
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Contributions

The article was drawn from the PhD thesis of SM. SM and MLM planned the study. SM implemented analyses of the data. FWCN and MLM supervised SM. MMS and MDM provided inputs on the interpretation of the results. MDM edited the article that was originally drafted by SM. All authors read and approved the final manuscript.

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Correspondence to S. Mdyogolo.

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Approval of the study was granted by the Animal Ethics Committee (AEC) of the Agricultural Research Council of South Africa (APIC18/03).

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Mdyogolo, S., MacNeil, M.D., Neser, F.W.C. et al. Assessing accuracy of genotype imputation in the Afrikaner and Brahman cattle breeds of South Africa. Trop Anim Health Prod 54, 90 (2022). https://doi.org/10.1007/s11250-022-03102-0

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