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Genomic evaluation of commercial herds with different pedigree structures using the single-step genomic BLUP in Nelore cattle

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Abstract

The aim of this work was to evaluate the impact of applying genomic information in pedigree uncertainty situations on genetic evaluations for growth- and cow productivity–related traits in Nelore commercial herds. Records for accumulated cow productivity (ACP) and adjusted weight at 450 days of age (W450) were used, as well as genotypes of registered and commercial herd animals, genotyped with the Clarifide Nelore 3.1 panel (~29,000 SNPs). The genetic values for commercial and registered populations were estimated using different approaches that included (ssGBLUP) or did not include genomic information (BLUP), with different pedigree structures. Different scenarios were tested, varying the proportion of young animals with unknown sires (0, 25, 50, 75, and 100%), and unknown maternal grandsires (0, 25, 50, 75, and 100%). The prediction accuracies and abilities were calculated. The estimated breeding value accuracies decreased as the proportion of unknown sires and maternal grandsires increased. The genomic estimated breeding value accuracy using the ssGBLUP was higher in scenarios with a lower proportion of known pedigree when compared to the BLUP methodology. The results obtained with the ssGBLUP showed that it is possible to obtain reliable direct and indirect predictions for young animals from commercial herds without pedigree structure.

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Data availability

The datasets generated and/or analyzed during the current study are available through the corresponding author upon reasonable request.

Code availability

The code generated during this study is available through the corresponding author upon reasonable request.

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Acknowledgements

The authors thank the National Association of Breeders and Researchers (ANCP, Ribeirão Preto, Brazil) for the support and data provided for this project.

Funding

This work was supported by the São Paulo Research Foundation, FAPESP (grant number 2016/22751-6).

Author information

Authors and Affiliations

  1. Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista Júlio de Mesquita Filho, Via de Acesso Prof. Paulo Donato Castellane s/n, CEP, Jaboticabal, SP, 14884-900, Brazil

    Marisol Londoño-Gil, Daniel Cardona-Cifuentes & Elisa Peripolli

  2. Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Av. Duque de Caxias Norte, 225m Campus Fernando Costa – USP, CEP, Pirassununga, SP, 13635-900, Brazil

    Rafael Espigolan & Fernando Baldi

  3. Associação Nacional de Criadores e Pesquisadores (ANCP), Rua João Godoy, 463, Jardim América, CEP, Ribeirão Preto, SP, 14020-230, Brazil

    Raysildo B. Lôbo

  4. Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, Av. Duque de Caxias Norte, 225 Campus Fernando Costa Jardim Elite, CEP, Pirassununga, SP, 13635-900, Brazil

    Angélica S. C. Pereira

  5. Instituto Nacional de Pesquisa Agropecuária (INIA), CEP 90200, Las Brujas, Uruguay

    Ignacio Aguilar

Authors
  1. Marisol Londoño-Gil
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  2. Daniel Cardona-Cifuentes
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  3. Rafael Espigolan
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  4. Elisa Peripolli
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  5. Raysildo B. Lôbo
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  6. Angélica S. C. Pereira
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  7. Ignacio Aguilar
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  8. Fernando Baldi
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Contributions

All authors contributed to the conception and design of the study. The preparation of the material, the data collection, and the analysis were carried out by all the authors. Marisol Londoño Gil wrote the first draft of the manuscript, and the other authors made their contributions on later versions. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Daniel Cardona-Cifuentes.

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Londoño-Gil, M., Cardona-Cifuentes, D., Espigolan, R. et al. Genomic evaluation of commercial herds with different pedigree structures using the single-step genomic BLUP in Nelore cattle. Trop Anim Health Prod 55, 95 (2023). https://doi.org/10.1007/s11250-023-03508-4

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