The power of comparative genomics is widely accepted and applies to all taxa (Sankoff and Nadeau 2000). The genomes of the model systems Arabidopsis (The Arabidopsis Genome Initiative 2000) and rice (Goff et al. 2002; Yu et al. 2002) have been completely sequenced and are used to aid in positional cloning of genes from related species having much larger genomes and lacking a complete genome sequence. Comparative mapping among nonmodel species helps to understand the evolution of plant genomes (Bennetzen and Freeling 1993; Gale and Devos 1998) and can help validate quantitative trait loci (QTL) from one crop species to another (Paterson et al. 1995). Although there is no known small genome model species in conifers to be the equivalent of Arabidopsis and rice, conifers would still benefit significantly from an organized comparative mapping effort.