Plant Systems Biology

Plant Systems Biology

The Plant Systems Biology Group seeks to explore and understand the network of genes, proteins, metabolites, and environmental signals that lead to complex phenotypes in DOE-relevant plant species.

Four Common gardens in Clatskanie (OR), Corvallis (OR), Boardman (OR) and Sedona (AZ) has been established for a population of 1,084Populus trichocarpa natural variants.  The resequencing efforts yield more than 28 million single nucleotide polymorphisms (SNPs), making it a very powerful resource to link genotypes to phenotypic traits through the genome-wide association studies (GWAS).  Plant morphology, architecture, photosynthesis parameters, disease response to cell wall chemistry, metabolites and gene expression have been identified.

Plant Systems Biology


Association mapping, transcriptomics, and transient expression identify candidate genes mediating plant–pathogen interactions in a tree

Invasive microbes causing diseases such as sudden oak death negatively affect ecosystems and economies around the world. The deployment of resistant genotypes for combating introduced diseases...

A 5-enolpyruvylshikimate 3-phosphate synthase functions as a transcriptional repressor in Populus

Long-lived perennial plants, with distinctive habits of inter-annual growth, defense, and physiology, are of great economic and ecological importance. However, some biological mechanisms resulting...

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that...

Capabilities & Research Areas

The group applies its expertise in plant physiology, development and evolution along with application of transcriptomics, proteomics, metabolomics, molecular genetics, spectroscopy, imaging and bioinformatics approaches to studying plant models ranging from perennial dicots and monocots (Populus, willow, EucalyptusAgave, switchgrass, and Brachypodium), to annuals (Arabidopsis) and Sphagnum mosses. Our current research portfolio includes projects centering on topics of bioenergy research, carbon fixation, allocation and cycling, responses to climate change, plant-microbe interactions and neutron and radiochemistry-based chemical in vivo imaging. The group collaborates with several DOE-funded labs (i.e. the Joint Genome Institute, Pacific Northwest National Lab, Brookhaven National Lab and National Renewable Energy Laboratory) and multiple academic institutions.


Jay Chen

Jay Chen

Plant Molecular Biologist and Geneticist