Compatibility of pedigree-based and marker-based relationship matrices for single-step genetic evaluation

Table 4 Parameter estimates and prediction performance obtained with simulated dataset 2

Parameters were estimated either, jointly using the full log-likelihood $\tilde{ℓ} = {\tilde{ℓ}}_{y ∣ m^{o}} + {\tilde{ℓ}}_{mark}$ , or by first estimating γ and $\tilde{s}$ using ${\tilde{ℓ}}_{mark}$ and then the other parameters using ${\tilde{ℓ}}_{y ∣ m^{o}}$ ; the last column contains parameter values estimated with the single-step method with an adjusted marker-based relationship matrix, in which first α and β were estimated using equation (6) and then the remaining parameters were estimated using $ℓ_{y ∣ m^{o}}$ ; the last two rows show the correlation between predicted and true breeding values, $Cor (\hat{a}, a)$ , for candidate boars, which is a measure of prediction performance, and the regression coefficient (reg) for the regression of a on $\hat{a}$ .

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