Plant height, branch structure, leaf display, wood production and wood gravity are important traits for the selection of superior tree types in forest improvement programs. These traits are inherently complex, determined by many genetic and environmental factors. The genetic factors, called quantitative trait loci (QTLs), are usually studied in an experimental cross derived from two parental lines through molecular mapping approaches. For many crops and model plant species, two phenotypically contrasting homozygous lines are crossed to generate an F1 progeny from which advanced generations, such as backcross, F2, or advanced intercross lines, are created for genetic mapping. The advantages of such a crossing procedure include the production of maximum disequilibria (i.e., non-random associations) between different loci and the precise characterization of a QTL allele from the marker alleles due to a known marker-QTL linkage phase. Because of these advantages, QTL mapping with an experimental cross has been instrumental for the identifi cation of genes in a variety of plants from annuals to perennials (Grattapaglia et al. 1996; Wu et al. 1998; Boerjan 2005; Paterson 2006; Li et al. 2006), and will continue to play a role in unraveling the genetic architecture of plant traits.