Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle

Bolormaa, S., Pryce, J. E., Kemper, K., Savin, K., Hayes, B. J., Barendse, W., Zhang, Y., Reich, C. M., Mason, B. A., Bunch, R. J., Harrison, B. E., Reverter, A., Herd, R. M., Tier, B., Graser, H. -U. and Goddard, M. E. (2013) Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle. Journal of Animal Science, 91 7: 3088-3104. doi:10.2527/jas.2012-5827


Author Bolormaa, S.
Pryce, J. E.
Kemper, K.
Savin, K.
Hayes, B. J.
Barendse, W.
Zhang, Y.
Reich, C. M.
Mason, B. A.
Bunch, R. J.
Harrison, B. E.
Reverter, A.
Herd, R. M.
Tier, B.
Graser, H. -U.
Goddard, M. E.
Title Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle
Formatted title
Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle
Journal name Journal of Animal Science   Check publisher's open access policy
ISSN 0021-8812
1525-3163
Publication date 2013
Sub-type Article (original research)
DOI 10.2527/jas.2012-5827
Open Access Status DOI
Volume 91
Issue 7
Start page 3088
End page 3104
Total pages 17
Place of publication Champaign, IL, United States
Publisher American Society of Animal Science
Language eng
Subject 1103 Clinical Sciences
1106 Human Movement and Sports Science
1311 Genetics
Abstract The aim of this study was to assess the accuracy of genomic predictions for 19 traits including feed efficiency, growth, and carcass and meat quality traits in beef cattle. The 10,181 cattle in our study had real or imputed genotypes for 729,068 SNP although not all cattle were measured for all traits. Animals included Bos taurus, Brahman, composite, and crossbred animals. Genomic EBV (GEBV) were calculated using 2 methods of genomic prediction [BayesR and genomic BLUP (GBLUP)] either using a common training dataset for all breeds or using a training dataset comprising only animals of the same breed. Accuracies of GEBV were assessed using 5-fold cross-validation. The accuracy of genomic prediction varied by trait and by method. Traits with a large number of recorded and genotyped animals and with high heritability gave the greatest accuracy of GEBV. Using GBLUP, the average accuracy was 0.27 across traits and breeds, but the accuracies between breeds and between traits varied widely. When the training population was restricted to animals from the same breed as the validation population, GBLUP accuracies declined by an average of 0.04. The greatest decline in accuracy was found for the 4 composite breeds. The BayesR accuracies were greater by an average of 0.03 than GBLUP accuracies, particularly for traits with known genes of moderate to large effect mutations segregating. The accuracies of 0.43 to 0.48 for IGF-I traits were among the greatest in the study. Although accuracies are low compared with those observed in dairy cattle, genomic selection would still be beneficial for traits that are hard to improve by conventional selection, such as tenderness and residual feed intake. BayesR identifed many of the same quantitative trait loci as a genomewide association study but appeared to map them more precisely. All traits appear to be highly polygenic with thousands of SNP independently associated with each trait.
Keyword Accuracy of genomic estimated breeding value
BayesR
Genomewide association study
Genomic best linear unbiased prediction
Multibreed
Single breed
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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