U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights


New Method for Identifying Genetic Regulatory Networks in Poplar
Published: November 26, 2013
Posted: March 27, 2014

Wood is an important renewable material for bioenergy and other industrial products, but its formation, a complex process regulated at many levels, is poorly understood. Such processes often involve interactions between regulatory genes known as transcription factors (TFs) and their direct DNA targets. These TF-DNA interactions constitute a regulatory hierarchy. To begin to understand these systems in poplar trees, researchers at North Carolina State University funded by the Department of Energy’s Genomic Science Program developed a robust, high-throughput pipeline to study the hierarchy of genetic regulation of wood formation using tissue-specific single cells known as protoplasts. A new method for isolating protoplasts from the wood-forming stem differentiating xylem (SDX) tissues of Populus trichocarpa was developed and used to study the expression of a specific poplar TF affecting wood formation. By integrating this novel system with computational approaches, a hierarchical layer of genes was inferred that was then functionally validated in SDX. This approach will be particularly useful in studying complex processes in plant species that lack mutants and a stable transformation system. It also can be used to improve forest tree productivity with more precise genetic approaches.

Reference: Lin, Y.-C., W. Li, Y.-H. Sun, S. Kumari, H. Wei, Q. Li, S. Tunlaya-Anukit, R. R. Sederoff, and V. L. Chiang VL. 2013. “SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa,” Plant Cell 25, 4324-41. DOI: 10.1105/tpc.113.117697. (Reference link)

Contact: Cathy Ronning, SC-23.2, (301) 903-9549
Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Plant Systems and Feedstocks, Plant-Microbe Interactions
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: Computational Biology, Bioinformatics, Modeling
  • Research Area: Research Technologies and Methodologies

Division: SC-23.2 Biological Systems Science Division, BER

 

BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

Aug 24, 2019
New Approach for Studying How Microbes Influence Their Environment
A diverse group of scientists suggests a common framework and targeting of known microbial processes [more...]

Aug 08, 2019
Nutrient-Hungry Peatland Microbes Reduce Carbon Loss Under Warmer Conditions
Enzyme production in peatlands reduces carbon lost to respiration under future high temperatures. [more...]

Aug 05, 2019
Amazon Forest Response to CO2 Fertilization Dependent on Plant Phosphorus Acquisition
AmazonFACE Model Intercomparison. The Science Plant growth is dependent on the availabi [more...]

Jul 29, 2019
A Slippery Slope: Soil Carbon Destabilization
Carbon gain or loss depends on the balance between competing biological, chemical, and physical reac [more...]

Jul 15, 2019
Field Evaluation of Gas Analyzers for Measuring Ecosystem Fluxes
How gas analyzer type and correction method impact measured fluxes. The Science A side- [more...]

List all highlights (possible long download time)