Increased prediction ability in Norway spruce trials using a marker x environment interaction and non-additive genomic selection model

A genomic selection (GS) study of growth and wood quality traits is reported based on control-pollinated Norway spruce families established in two Northern Swedish trials at two locations using exome capture as a genotyping platform. Non-additive effects including dominance and first-order epistatic interactions (including additive by additive, dominance by dominance, and additive by dominance) and marker-by-environment interaction (M×E) effects were dissected in genomic and phenotypic selection models. GS models partitioned additive and non-additive genetic variances more precisely compared with pedigree-based models. In addition, predictive ability (PA) in GS was substantially increased by including dominance and slightly increased by including M×E effects when these effects are significant. For velocity, response to GS (RGS) per year increased 91.3/43.7%, 86.9/82.9%, and 78.9/80.8% compared with response to phenotypic selection (RPS) per year when GS was based on 1) main marker effects (M), 2) M + M×E effects (A), and 3) A + dominance effects (AD) for site 1/site 2, respectively. This indicates that including M×E and dominance effects not only improves genetic parameter estimates but also may improve the genetic gain when they are significant. For tree height, Pilodyn, and modulus of elasticity (MOE), RGS per year improved up to 84.2%, 91.3%, and 92.6% compared with RPS per year, respectively.