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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-33.2 Biological Systems Science Division, BER

 

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