Populus responses to edaphic and climatic cues: Emerging evidence from systems biology research

The emergence of Populus as a model system for tree biology continues to be driven by a community of scientists dedicated to developing the resources needed to undertake genetic and functional genomic studies in this genus. As a result, understanding the molecular processes that underpin the growth and development of cottonwood, aspen, and hybrid poplar has steadily increased over the last several decades. Recently, our ability to examine the basic mechanisms whereby trees respond to a changing climate and resource limitations has benefited greatly from the sequencing of the P. trichocarpa genome. This landmark event has laid a solid foundation upon which biologists can now quantify, in breathtaking and unprecedented detail, the diversity of genes, proteins, and metabolites that govern the growth and development of some of the longest living and tallest growing organisms on Earth. Although the challenges likely to be encountered by scientists who work with trees are many, recent literature provides a few examples where a systems approach, one that focuses on integrating transcriptomic, proteomic, and metabolomic analyses, is beginning to provide insights into the molecular-scale response of poplars to their climatic and edaphic environment. In this review, our objectives are to look at evidence from studies that examine the molecular response of poplar to edaphic and climatic cues and highlight instances where two or more omic-scale measurements confirm and hopefully expand our inferences about mechanisms contributing to observed patterns of response. Based on conclusions drawn from these studies, we propose that three requirements will be essential as systems biology in poplar moves to reveal unique insights. These include use of genetically-defined individuals (e.g., pedigrees or transgenics) in studies; incorporation of modeling as a complement to transcriptomic, proteomic and metabolomic data; and inclusion of whole-tree and stand-level phenotypes to place molecular-scale insights into a real-world context.