Genomic selection validated across two generations of loblolly pine breeding

Abstract

This study evaluated the effectiveness of genomic selection (GS) in loblolly pine (Pinus taeda) using a two-generation closed breeding population and a genetically diverse Mainline population. Single-step genomic best linear unbiased prediction (ssGBLUP) models were used to include all phenotypic, genotypic, and pedigree information. Prediction accuracies of genomic estimated breeding values reached up to 0.70 for stem volume and stem straightness. Prediction accuracy showed a strong linear relationship with mean relatedness between training and validation populations (r > 0.92). Adjusting the scaling between genomic and pedigree relationship matrices improved model stability, increased prediction accuracy, and reduced bias in genomic estimated breeding values. Estimates of heritability and variance components from ssGBLUP were consistent with pedigree-based models, particularly when genomic relationships were properly scaled. Genomic selection had approximately 50% more genetic gain per year relative to conventional selection. Overall, these results demonstrate that GS can be effectively integrated into operational conifer breeding programs, given sustained investment in large, well-connected training populations with high-quality phenotypic data. We also outline the planned implementation of GS in the North Carolina State University Cooperative Tree Improvement Program to increase genetic gain.