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This estimate is referred to as a molecular breeding value (MBV).
Genomic prediction (GP) estimates the genetic merit, as a molecular breeding value (mBV), for each trait based on many SNPs.
Accuracies of molecular breeding values were estimated based on the genetic correlation between the molecular breeding value and trait phenotype.
For the selection index, the molecular breeding value g was considered as a separate trait, which is correlated to the breeding value it predicts, with the correlation between ai and gi (r aigi ) equal to the accuracy of the molecular breeding value; the heritability of g was equal to 0.999.
We combined phenotypic information with genomic predictions of breeding value, i.e. the molecular breeding value (g), from both PB and CB information sources to estimate breeding values for PB (aPB) and CB (a CB ) performances.
However, this assessment was based on comparisons for which the molecular breeding value (mbv) was combined with PB phenotypic information only, and the mbv was based on either PB or CB individuals with phenotypes, but not on both.
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With one exception, the estimated genetic correlations of within-breed molecular breeding values with trait phenotype were greater than 0.28 when evaluated in the breed used for training.
Even for closely related breeds, within- or across-breed trained molecular breeding values have limited prediction accuracy for breeds that were not in the training set.
For breeds in the training set, across- and within-breed trained molecular breeding values had similar accuracies.
Most estimated genetic correlations for the across-breed trained molecular breeding values were moderate (> 0.30).
This issue is of importance to the development of prediction equations for molecular breeding values in across-breed analyses, because the ASEs estimated for QTL regions will be averaged across breeds that segregate and those that do not segregate for certain QTL, which will limit the accuracy of molecular estimates of breeding value.
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