Plant Genomics Group

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The Plant Genomics Group seeks to explore and understand the network of genes, proteins, metabolites, and environmental signals that lead to complex phenotypes in forest trees. Our systems biology approach relies upon modern molecular genetics and genomics techniques and focuses on black cottonwood, Populus trichocarpa, as the reference organism. We strive to integrate (conceptually and through the use of multi-scale models) whole-plant, cellular and subcellular studies of tree growth and development in an effort to address the plant- and ecosystem-based energy and environmental needs of the country.

Group Updates:

• Winner of the Best Poster Award for Laboratory Directed R&D projects goes to Udaya Kalluri of the Environmental Sciences Division for her poster “Unraveling Regulatory and Biosynthetic Genes that Control Cellulose Production in the Model Bioenergy Crop Populus.”
  
  Image: LDRD poster winer Udaya Kalluri (left) pictured with Lab Director Thom Mason(right)
• ORNL, Los Alamos pioneer new approach to assist scientists, farmers
  OAK RIDGE, Tenn., Nov. 19, 2009 - Sustainable farming, initially adopted to preserve soil quality for future generations, may also play a role in maintaining a healthy climate, according to researchers at the Department of Energy's Oak Ridge and Los Alamos national laboratories.
  
  Novel Multivariate Analysis for Soil Carbon Measurements using Laser-Induced Breakdown Spectroscopy [abstract][article]
  Martin, M. Z., Labbe, N., Andre, N., Wullschleger, S. D., Harris, R. D., and Ebinger, M. H.
• ORNL scientists report the most comprehensive characterization of the subcellular proteome of Populus xylem.
  • Kalluri U, Hurst G, Lankford P, Ranjan P and Pelletier D, “Shotgun profiling of Populus developing xylem proteome”, Proteomics Journal (5.5). 9 (21): 4871 - 4880 (2009). [abstract]
  • Journal cover: an article by Kalluri et al. contributed to the cover art on the latest issue of Proteomics journal (impact factor ~5.5).
• Plant Systems Biology group intern, Anjali Bisaria’s poster was selected from among DOE SULI submissions to attend the 2009 National Science and Energy Research Challenge (SERCh) to be held on 9th November. Anjali was mentored by Udaya Kalluri.
  Update: Anjali Bisaria took 3rd place in the Environmental Sciences category of the SERCh, which included a $1,000 scholarship prize.
• Special Issue: Poplar Community Genomics - Volume 28 Issue 5 2009
  in Critical Reviews in Plant Sciences
  • Populus Community in Mega-Genomics: Coming of Age
    Zong-Ming Cheng; Gerald A. Tuskan
  • Poplar Genomics: State of the Science
    Xiaohan Yang; Udaya C. Kalluri; Stephen P. DiFazio; Stan D. Wullschleger; Timothy J. Tschaplinski; Max Zong-Ming Cheng; Gerald A. Tuskan
  • Populus Responses to Edaphic and Climatic Cues: Emerging Evidence from Systems Biology Research
    Stan D. Wullschleger; David J. Weston; John M. Davis
  • Genomics of Secondary Metabolism in Populus: Interactions with Biotic and Abiotic Environments
    Feng Chen; Chang-Jun Liu; Timothy J. Tschaplinski; Nan Zhao
• Publication: Gene expression profiling: opening the black box of plant ecosystem responses to global change in Global Change Biology.
  (Figure 1. From Article) Schematic describing the integration of plant, community,and ecosystem responses to an element of global change.Elements of global change directly impact molecular, biochemical, and physiological processes (red arrows), which combine to determine whole plant performance. Genotypic variation in whole plant responses drives ecological interactions that underlie community and ecosystem responses to global change. Feedbacks from larger scales of organization (dashed arrows) impact individual plant performance via effects on resource availability and disturbance that modify the direct effects on global change on plant function. Transcript profiling and high-throughput biochemical and physiological screening provide an opportunity to better understand the ?black box? of mechanisms driving plant responses to various elements of global change under field conditions.
Job Announcement: The Environmental Sciences Division (ESD) at Oak Ridge National Laboratory (ORNL) seeks a plant molecular biologist/geneticist to contribute to our systems biology program. This program is focused on energy and environmental applications of modern-day plant genetics and genomics. Opportunities are available to identify candidate genes and undertake functional gene analysis using emerging tools of plant genomics. An interest in functional and comparative genomics, quantitative trait loci analysis, association studies, and a strong quantitative genetics background will be viewed favorably. The candidate will have the opportunity to initiate his or her own research projects in addition to participating with ESD staff on existing projects. Early and mid-career positions are available.
Nancy Engle was the recipient of the 2008 Technical Support Award in the Environmental Sciences Division in recognition of her outstanding productivity, organic synthesis skills, ability to collaborate effectively in a team setting, and continued professional growth that serve ORNL's metabolomics research activities.
Press Release: Researchers discover primer to plant defense system.
OAK RIDGE, Tenn., April 3, 2009 -- By identifying a novel compound that primes a plant's immune system, researchers at Oak Ridge National Laboratory and the University of Chicago may be on a path to developing disease-resistant plants.
Udaya Kalluri, research scientist in the Plant Systems Biology Group, was the recipient of the 24th Annual YWCA Tribute to Women award in the category of science and technology (via Knox News).
Xiaohan Yang receives the 2007 Distinguished Achievement Award for post-doctoral research from Gray Jacobs, Director of the Environmental Sciences Division
Supplemental material for F-box manuscript, Yang et al.
Genome structure and emerging evidence of an incipient sex chromosome in Populus. Tongming Yin, Stephen P. DiFazio, Lee E. Gunter, Xinye Zhang, Michell M. Sewell, Scott A. Woolbright, Gery J. Allan, Collin T. Kelleher, Carl J. Douglas, Mingxiu Wang, and Gerald A. Tuskan
Lee Gunter from the ORNL Plant Systems Biology group receives the 2007 Technical Support Award from Gary Jacobs, Director of the Environmental Sciences Division.
Connecting Genes, Coexpression Modules, and Molecular Signatures to Environmental Stress Phenotypes in Plants. David J. Weston, Lee E. Gunter, Alistair Rogers, and Stan D. Wullschleger BMC Systems Biology 2008, 2:16doi:10.1186/1752-0509-2-16 Published: 4 February 2008.