Increased prediction ability in Norway spruce trials using a marker x environment interaction and non-additive genomic selection model
J Hered. 2019 Oct 20 [Epub ahead of print]
Chen ZQ, Baison J, Pan J, Westin J, García Gil MR, Wu HX

Abstract
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 than 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 78.9/80.8%, 86.9/82.9%, and 91.3/88.2% 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 sites 1 and 2, respectively. This indicates that including M×E and dominance effects not only improves genetic parameter estimates but also when they are significant may improve the genetic gain. For tree height, Pilodyn, and modulus of elasticity (MOE), RGS per year improved up to 68.9%, 91.3%, and 92.6% compared with RPS per year, respectively.

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