Best linear prediction of breeding values in a forest tree improvement program

Best Linear Prediction (BLP) was used to predict breeding values for 1,396 parents from progeny test data in an operational slash pine breeding program. BLP rankings of parents were compared to rankings of averaged standard scores, a common approach in forestry. Using BLP rankings, selection of higher ranking parents tends to choose parents in a larger number of more precise progeny tests. The trend is the opposite with standard scores; higher ranking parents tend to be those in fewer, less precise tests. BLP and a related methodology, Best Linear Unbiased Prediction (BLUP), were developed by dairy cattle breeders and have not been used widely outside of animal breeding for predicting breeding values from messy progeny test data. Application of either of these techniques usually requires simplifying assumptions to keep the problem computationally tractable. The more appropriate technique for a given application depends upon which set of assumptions are better for the given problem. An assumption of homogeneous genetic and error variances and covariances, generally made by animal breeders when applying BLUP, was inappropriate for our data. We employed an approach that treated fixed effects as known and treated the same trait measured in different environments as different traits with heterogeneous variance structures. As tree improvement programs become more complex, the ease with which BLP and BLUP handle messy data and incorporate diverse sources of information should make these techniques appealing to forest tree breeders.