Functional genomics and cell wall biosynthesis in loblolly pine

Loblolly pine (Pinus taeda L.) is the most widely planted tree species in t he USA and an important tree in commercial forestry world-wide. The large g enome size and long generation time of this species present obstacles to bo th breeding and molecular genetic analysis. Gene discovery by partial DNA s equence determination of cDNA clones is an effective means of building a kn owledge base for molecular investigations of mechanisms governing aspects o f pine growth and development, including the commercially relevant properti es of secondary cell walls in wood. Microarray experiments utilizing pine c DNA clones can be used to gain additional information about the potential r oles of expressed genes in wood formation. Different methods have been used to analyze data from first-generation pine microarrays, with differing deg rees of success. Disparities in predictions of differential gene expression between cDNA sequencing experiments and microarray experiments arise from differences in the nature of the respective analyses, but both approaches p rovide lists of candidate genes which should be further investigated for po tential roles in cell wall formation in differentiating pine secondary xyle m. Some of these genes seem to be specific to pine, while others also occur in model plants such as Arabidopsis, where they could be more efficiently investigated.