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

Research Article

John C. McEwan¹  Wendy E. Bain¹  Ken G. Dodds¹  Shannon M. Clarke¹  Flávio S. Schenkel²  Stephen P. Miller³  Luiz F. Brito³  Mehdi Sargolzaei⁴  Natalie K. Pickering⁵ 

[1] AgResearch, Invermay Agricultural Centre, Private Bag 50034, 9053, Mosgiel, New Zealand;Centre for Genetic Improvement of Livestock, University of Guelph, N1G2W1, Guelph, Canada;Centre for Genetic Improvement of Livestock, University of Guelph, N1G2W1, Guelph, Canada;AgResearch, Invermay Agricultural Centre, Private Bag 50034, 9053, Mosgiel, New Zealand;Centre for Genetic Improvement of Livestock, University of Guelph, N1G2W1, Guelph, Canada;The Semex Alliance, N1H6J2, Guelph, Canada;Focus Genetics, 4110, Napier, New Zealand;

关键词: GBLUP;    Ovine HD SNP Chip;    Genomic selection;    Eating quality traits;   

DOI  :  10.1186/s12863-017-0476-8

 received in 2016-10-11, accepted in 2017-01-13,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundNew 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.ResultsThe 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.ConclusionsThe 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.

【 授权许可】

CC BY   
© The Author(s). 2017

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