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Evaluation of the International Society for Animal Genetics bovine single nucleotide polymorphism parentage panel in South African Bonsmara and Drakensberger cattle

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Abstract

A panel of 200 single nucleotide polymorphisms (SNPs) have been recommended by the International Society for Animal Genetics (ISAG) for use in parentage verification of cattle. While the SNPs included on the ISAG panel are segregating in European Bos taurus and Bos indicus breeds, their applicability in South African (SA) Sanga cattle has never been evaluated. This study, therefore, assessed the usefulness of the ISAG panel in SA Bonsmara (BON) and Drakensberger (DRB) cattle. Genotypes of 185 ISAG SNPs from 64 BON and 97 DRB sire-offspring pairs were available, all of which were validated with 119,375 SNPs. Of the 185 ISAG SNPs, 14 and 18 in the BON and DRB, respectively (9 in common to both breeds), were either monomorphic, exhibited at least one discordance between validated sire-offspring pairs, or had poor call rate or clustering issue. The mean minor allele frequency of the 185 ISAG SNPs was 0.331 in the BON and 0.359 in the DRB. The combined probability of parentage exclusion (PE) was the same (99.46%) for both breeds, while the probability of identity varied from 1.61 × 10−48 (BON) to 1.11 × 10−54 (DRB). Fifteen (23.4%) and 32 (33%) of the already validated sire-offspring pairs for the BON and DRB, respectively, were determined by the ISAG panel to be false-negatives based on a threshold of having at least two discordant SNPs. In comparison to sire discovery using the 119,375 SNPs, sire discovery using only the ISAG panel identified correctly 44 (out of 64 identified using the 119,375 SNPs) unique sire-offspring BON pairs and 62 (out of 97 identified using the 119,375 SNPs) unique sire-offspring DRB when all sires were masked. Five BON and three DRB offspring had > 1 sire nominated. This study demonstrated that the use of the ISAG panel may result in incorrect exclusions and multiple candidate sires for a given animal. Selection of more informative SNPs is, therefore, necessary in the pursuit of a low-cost and effective SNP panel for indigenous cattle breeds in SA.

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Acknowledgments

We wish to thank the South African Bonsmara and Drakensberger Cattle Breeders Societies for providing access to their genotype and pedigree databases available at the Agricultural Research Council (ARC) and South African Studbook.

Funding

The authors would like to acknowledge the funding from the Technology Innovation Agency (TIA) provided to the Beef Genomics Project (BGP). The authors express their gratitude to the projects funded by the Red Meat Research and  Development of South Africa (RMRD SA) under the University of Pretoria (UP) that donated with the genotypes. This research project was also financially supported by the ARC, National Research Foundation (NRF), and the UP.

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Authors and Affiliations

  1. Department of Animal and Wildlife Science, University of Pretoria, Hatfield, Pretoria, 0002, South Africa

    Yandisiwe P. Sanarana, Donagh P. Berry & Este van Marle-Köster

  2. Agricultural Research Council-Animal Production, Irene, Pretoria, 0062, South Africa

    Yandisiwe P. Sanarana, Azwihangwisi Maiwashe & Cuthbert Banga

  3. Teagasc, Animal & Grassland Research and Innovation Center, Moorepark, Fermoy, Co. Cork, Ireland

    Donagh P. Berry

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  1. Yandisiwe P. Sanarana
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Correspondence to Yandisiwe P. Sanarana.

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Sanarana, Y.P., Maiwashe, A., Berry, D.P. et al. Evaluation of the International Society for Animal Genetics bovine single nucleotide polymorphism parentage panel in South African Bonsmara and Drakensberger cattle. Trop Anim Health Prod 53, 32 (2021). https://doi.org/10.1007/s11250-020-02481-6

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