ORIGINAL ARTICLE Effect of genomic prediction on response to selection in forest tree breeding J. Stejskal 1 & M. Lstibůrek 1 & J. Klápště 1,2 & J. Čepl 1 & Y. A. El-Kassaby 3 Received: 15 May 2017 /Revised: 1 August 2018 /Accepted: 12 August 2018 /Published online: 11 September 2018 # Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Through stochastic simulations, estimates of breeding values accuracies and response to selection were assessed under traditional pedigree-based and genomic-based evaluation methods. More specifically, several key parameters such as the trait’ s heritability (0.2 and 0.6), the number of QTLs underlying the trait (100 to 200), and the marker density (1 to 10 SNPs/cM) were evaluated. Additionally, impact of two contrasting mating designs (partial diallel vs. single-pair mating) was investigated. Response to selection was then assessed in a seed production population (seed orchard consisting of unrelated selections) for different effective population sizes (N e = 5 to 25). The simulated candidate population comprised a fixed size of 2050 individuals with fast linkage disequilibrium decay, generally found in forest tree populations. Following the genetic/genomic evaluation, top- ranked individuals were selected to meeting the predetermined effective population size in target production population. The combination of low h 2 , high N e , and dense marker coverage resulted at maximum relative genomic prediction efficiency and the most efficient exploitation of the Mendelian sampling term (within-family additive genetic variance). Since genomic prediction of breeding values constitutes the methodological foundation of genomic selection, our results can be used to address important questions when similar scenarios are considered. Keywords GBLUP . Seed orchards . Genomic selection . Response to selection . Effective population size Introduction The effectiveness of genomic selection (GS) is contingent on populating the genome with dense marker coverage to exploit the associations between markers and causal variants (a.k.a. linkage disequilibrium (LD)) for selection and breeding purposes (Meuwissen et al. 2001). From its inception, GS has garnered increased attention and acceptance for its poten- tial in predicting individuals’ genetic values and the delivery of greater gains per unit time and cost. The impetus of GS coincided with the development of efficient, accurate, and relatively affordable high throughput single-nucleotide poly- morphism (SNP) genotyping technologies (Elshire et al. 2011; Peterson et al. 2012; Truong et al. 2012). GS is a significant paradigm shift with an inconceivable repercussion as the models’ unit of quantitative genetics analyses have shifted from being the line of descent to the allele. Thus, the tradi- tional approach of genetic evaluation which fundamentally is based on the pedigree expected relationship is replaced with the actual realized relationship (Wright 1922; VanRaden 2008). Genomic best linear unbiased prediction (GBLUP) has been used to estimate the genomic estimated breeding values (GEBVs) of various complex traits in human, plant, and animal populations (Yang et al. 2010; Heffner et al. 2009; Villanueva et al. 2005; VanRaden 2008) ranging from cattle to aquacultures (Sonesson and Meuwissen 2009; Ødegård and Meuwissen 2015; Vela-Avitúa et al. 2015). Several studies described how genomic BLUP differs from Communicated by A. A. Myburg Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11295-018-1283-8) contains supplementary material, which is available to authorized users. * J. Stejskal stejskalj@fld.czu.cz 1 Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, 165 21 Prague, Czech Republic 2 Scion (New Zealand Forest Research Institute Ltd.), 49 Sala Street, Whakarewarewa, Rotorua 3010, New Zealand 3 Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada Tree Genetics & Genomes (2018) 14: 74 https://doi.org/10.1007/s11295-018-1283-8