When the Tree Let Us See the Forest: Systems Biology and Natural Variation Studies in Forest Species

Abstract

Systems biology has emerged in the last years as a comprehensive set of tools which provides rich biological information by integrating different cell organization levels (genome, epigenome, transcripts, proteins, and metabolites) and providing not only the relationships and correlations among them but also giving the possibility of modeling how and why cells and tissues are plastic to different environments. To perform this characterization, several analytical methods (NGS, mass spectrometry) and statistical and modeling tools must be used. Contrary to classic targeted approaches, the untargeted analyses of a plant system far from introducing noise or scattering the focus of the research can provide new candidates, pathways, or counterintuitive mechanisms otherwise undetectable. In this chapter, we briefly describe methodology and applications of systems biology by using three different studies: natural variation of the metabolome of Pinus pinaster and its relation to different geographic origins and wood quality traits and how Pinus radiata adapt to thermal or ultraviolet stresses. These examples illustrate how systems biology can contribute toward the full understanding of the biological processes mediating tree stress adaption and development, and forest ecology, besides constituting a powerful tool for breeders toward the selection of specific donors for specific environments, or model how new mixtures of genotypes will impact over forestry demanding traits.