BMCGenetics2017 Brito-GenomicPrediction.pdf (994.42 kB)

Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip

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posted on 2023-05-03, 21:07 authored by Luiz Brito, Shannon ClarkeShannon Clarke, John McEwanJohn McEwan, Stephen Miller, Natalie Pickering, Wendy BainWendy Bain, Ken Dodds, Mehdi Sargolzaei, Flavio Schenkel
Background: New Zealand has some unique Terminal Sire composite sheep breeds, which were developed in the last three decades to meet commercial needs. These composite breeds were developed based on crossing various Terminal Sire and Maternal breeds and, therefore, present high genetic diversity compared to other sheep breeds. Their breeding programs are focused on improving carcass and meat quality traits. There is an interest from the industry to implement genomic selection in this population to increase the rates of genetic gain. Therefore, the main objectives of this study were to determine the accuracy of predicted genomic breeding values for various growth, carcass and meat quality traits using a HD SNP chip and to evaluate alternative genomic relationship matrices, validation designs and genomic prediction scenarios. A large multi-breed population (n = 14,845) was genotyped with the HD SNP chip (600 K) and phenotypes were collected for a variety of traits. Reults: The average observed accuracies (± SD) for traits measured in the live animal, carcass, and, meat quality traits ranged from 0.18 ± 0.07 to 0.33 ± 0.10, 0.28 ± 0.09 to 0.55 ± 0.05 and 0.21 ± 0.07 to 0.36 ± 0.08, respectively, depending on the scenario/method used in the genomic predictions. When accounting for population stratification by adjusting for 2, 4 or 6 principal components (PCs) the observed accuracies of molecular breeding values (mBVs) decreased or kept constant for all traits. The mBVs observed accuracies when fitting both G and A matrices were similar to fitting only G matrix. The lowest accuracies were observed for k-means cross-validation and forward validation performed within each k-means cluster. Conclusions: The accuracies observed in this study support the feasibility of genomic selection for growth, carcass and meat quality traits in New Zealand Terminal Sire breeds using the Ovine HD SNP chip. There was a clear advantage on using a mixed training population instead of performing analyzes per genomic clusters. In order to perform genomic predictions per breed group, genotyping more animals is recommended to increase the size of the training population within each group and the genetic relationship between training and validation populations. The different scenarios evaluated in this study will help geneticists and breeders to make wiser decisions in their breeding programs.


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© The Author(s). 2017. International License ( which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated.


  • English

Does this contain Māori information or data?

  • No


BioMed Central

Journal title

BMC Genetics




Brito, L. F., Clarke, S. M., McEwan, J. C., Miller, S. P., Pickering, N. K., Bain, W. E., Dodds, K. G., Sargolzaei, M., & Schenkel, F. S. (2017). Prediction of genomic breeding values for growth, carcass and meat quality traits in a multi-breed sheep population using a HD SNP chip. BMC Genetics, 18, 7. doi:10.1186/s12863-017-0476-8

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