Tree Genetics & Genomes (2010) 6:591–600 DOI 10.1007/s11295-010-0274-1 ORIGINAL PAPER Impact of reconstructed pedigrees on progeny-test breeding values in red spruce Trevor K. Doerksen · Christophe M. Herbinger Received: 24 November 2008 / Revised: 28 November 2009 / Accepted: 26 January 2010 / Published online: 18 February 2010 © Springer-Verlag 2010 Abstract Pedigrees reconstructed through DNA marker assigned paternities in polymix (PMX) and open pollinated (OP) progeny tests were analyzed using mixed models to test the effect of unequal male reproductive success and pedigree errors on quantitative genetic parameters. The reconstructed pedigree increased heritabilities in the larger PMX test. Increased heritability resulted from adding the paternities to the pedigree per se, not by correcting the male reproductive bias by specifying the exact pedigree. Removing hypothesized pedigree errors had no effect on quantitative parameters, either because the magnitude of the errors was too small (PMX) or the progeny test was too small to detect variance components reliably (OP). Although there was no advantage in backwards selection, the increased additive variance, heritabilities and accuracy of progeny with assigned paternities in the pedigree, should permit forward selection of offspring with greater genetic gain and complete control of coancestry for future breeding decisions. Some possible breeding population structures with the new genetic information are discussed. Communicated by A. Kremer T. K. Doerksen (B ) · C. M. Herbinger Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS B3L 3Z8, Canada e-mail: Trevor.Doerksen@NRCan-RNCan.gc.ca Present Address: T. K. Doerksen Natural Resources Canada, Laurentian Forestry Centre, 1055 du P.E.P.S., P.O. Box 10380 Succ. Sainte-Foy, Québec, Québec, G1V 4C7 Canada Keywords Pedigree reconstruction · Paternity · BLUP · Coancestry · Spruce Introduction Forest genetic tests have traditionally been used to rank parents for backwards selection. Although for- ward, within-family selection is necessary for recur- rent population improvement, there is some contro- versy whether forward selected progenies should be used directly in the production population because of their lower breeding value accuracy (Ruotsalainen and Lindgren 1998; Burdon and Kumar 2004). Accuracy can be increased by increasing the number of tested sibs per family, clonal testing (Shaw and Hood 1985; Kumar 2006) or using more efficient statistical test designs (John and Williams 1998), but these must be applied prior to implementing tests. Alternatively, retrospec- tive analysis of quantitative data using mixed model methodology can make more efficient use of limited resources allocated to breeding programs by adjusting records for microsite spatial variation (Joyce et al. 2002), identifying causal sources of genotype by envi- ronment interaction variation (Frensham et al. 1998) or better modeling of the true underlying pedigree structure. Progenies of polymix (PMX) and open-pollinated (OP) forest genetic tests are usually assumed to be related as half-sibs (relationship coefficient= r = 0.25) but in reality a more complex pedigree exists as the re- sult of male differential reproductive success (Wheeler et al. 2006; Doerksen and Herbinger 2008) and in- breeding (Squillace 1974; Sorensen and White 1988). The unidentified contributions of males to the pedigree