Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation

Daetwyler, Hans D., Swan, Andrew A., van der Werf, Julius H. J. and Hayes, Ben J. (2012) Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation. Genetics Selection Evolution, 44 . doi:10.1186/1297-9686-44-33


Author Daetwyler, Hans D.
Swan, Andrew A.
van der Werf, Julius H. J.
Hayes, Ben J.
Title Accuracy of pedigree and genomic predictions of carcass and novel meat quality traits in multi-breed sheep data assessed by cross-validation
Journal name Genetics Selection Evolution   Check publisher's open access policy
ISSN 1297-9686
Publication date 2012-11-12
Sub-type Article (original research)
DOI 10.1186/1297-9686-44-33
Open Access Status DOI
Volume 44
Total pages 11
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Formatted abstract
Background: Genomic predictions can be applied early in life without impacting selection candidates. This is especially useful for meat quality traits in sheep. Carcass and novel meat quality traits were predicted in a multi-breed sheep population that included Merino, Border Leicester, Polled Dorset and White Suffolk sheep and their crosses.
Methods. Prediction of breeding values by best linear unbiased prediction (BLUP) based on pedigree information was compared to prediction based on genomic BLUP (GBLUP) and a Bayesian prediction method (BayesR). Cross-validation of predictions across sire families was used to evaluate the accuracy of predictions based on the correlation of predicted and observed values and the regression of observed on predicted values was used to evaluate bias of methods. Accuracies and regression coefficients were calculated using either phenotypes or adjusted phenotypes as observed variables.
Results and conclusions. Genomic methods increased the accuracy of predicted breeding values to on average 0.2 across traits (range 0.07 to 0.31), compared to an average accuracy of 0.09 for pedigree-based BLUP. However, for some traits with smaller reference population size, there was no increase in accuracy or it was small. No clear differences in accuracy were observed between GBLUP and BayesR. The regression of phenotypes on breeding values was close to 1 for all methods, indicating little bias, except for GBLUP and adjusted phenotypes (regression = 0.78). Accuracies calculated with adjusted (for fixed effects) phenotypes were less variable than accuracies based on unadjusted phenotypes, indicating that fixed effects influence the latter. Increasing the reference population size increased accuracy, indicating that adding more records will be beneficial. For the Merino, Polled Dorset and White Suffolk breeds, accuracies were greater than for the Border Leicester breed due to the smaller sample size and limited across-breed prediction. BayesR detected only a few large marker effects but one region on chromosome 6 was associated with large effects for several traits. Cross-validation produced very similar variability of accuracy and regression coefficients for BLUP, GBLUP and BayesR, showing that this variability is not a property of genomic methods alone. Our results show that genomic selection for novel difficult-to-measure traits is a feasible strategy to achieve increased genetic gain.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ
Additional Notes Article number 33

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