Single-Step Genomic Analysis Increases the Accuracy of Within-Family Selection in a Clonally Replicated Population of Pinus taeda L.
Abstract The use of genomic markers in forest tree breeding is expected to improve the response to selection, especially within family. To evaluate the potential improvements from genotyping, we analyzed a large Pinus taeda L. clonal population (1,831 cloned individuals) tested in multiple environments. Of the total, 723 clones from five full-sib families were genotyped using 10,337 single-nucleotide polymorphism markers. Single-step models with genomic and pedigree-based relationships produced similar heritability estimates. Breeding value predictions were greatly improved with inclusion of genomic relationships, even when clonal replication was abundant. The improvement was limited to genotyped individuals and attributable to accounting for the Mendelian sampling effect. Reducing clonal replication by omitting data indicated that genotyping improved breeding values similar to clonal replication. Genomic selection predictive ability (masking phenotypes) was greater for stem straightness (0.68) than for growth traits (0.41 to 0.44). Predictive ability for a new full-sibling family was poorer than when full-sibling relationships were present between model training and validation sets. Species that are difficult to propagate clonally can use genotyping to improve within-family selection. Clonal testing combined with genotyping can produce breeding value accuracies adequate to graft selections directly into deployment orchards without progeny testing. Study Implications Genomic markers can improve the reliability of breeding values, resulting in a more confident ranking of individuals within families. For genotyped individuals, the improvements were comparable to clonal testing. Breeding programs for species that are difficult to propagate clonally should consider genotyping to replace or supplement clonal testing as a means to improve within-family selection. For genomic prediction of breeding values without phenotypes (genomic selection), a robust genetic relationship between model training and validation sets is required. The single-step model allows genotyping a subset of the population and is a straightforward extension of well-established methods.