Genomic selection for resistance to mammalian bark stripping and associated chemical compounds in radiata pine

The integration of genomic data into genetic evaluations can facilitate the rapid selection of superior genotypes and accelerate the breeding cycle in trees. In this study, 390 trees from 74 control-pollinated families were genotyped using a 36K Axiom SNP array. A total of 15,624 high-quality SNPs were used to develop genomic prediction models for mammalian bark stripping, tree height, and selected primary and secondary chemical compounds in the bark. Genetic parameters from different genomic prediction methods—single-trait best linear unbiased prediction based on a marker-based relationship matrix (genomic best linear unbiased prediction), multitrait single-step genomic best linear unbiased prediction, which integrated the marker-based and pedigree-based relationship matrices (single-step genomic best linear unbiased prediction) and the single-trait generalized ridge regression—were compared to equivalent single- or multitrait pedigree-based approaches (ABLUP). The influence of the statistical distribution of data on the genetic parameters was assessed. Results indicated that the heritability estimates were increased nearly 2-fold with genomic models compared to the equivalent pedigree-based models. Predictive accuracy of the single-step genomic best linear unbiased prediction was higher than the ABLUP for most traits. Allowing for heterogeneity in marker effects through the use of generalized ridge regression did not markedly improve predictive ability over genomic best linear unbiased prediction, arguing that most of the chemical traits are modulated by many genes with small effects. Overall, the traits with low pedigree-based heritability benefited more from genomic models compared to the traits with high pedigree-based heritability. There was no evidence that data skewness or the presence of outliers affected the genomic or pedigree-based genetic estimates.