Plant Genomics Group

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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. 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, Switchgrass, Brachypodium and Agave) to annuals (Arabidopsis) to mosses. Our current research portfolio includes projects centering on topics of bioenergy research, carbon fixation, allocation and cycling, responses to climate change, plant-microbe interaction and neutron and radiochemistry-based chemical in vivo imaging. The group collaborates with several DOE-funded (i.e. Pacific Northwest National Lab, Brookhaven National Lab and National Renewable Energy Laboratory) and other academic institutes.

Group Updates:

• Gerald A. Tuskan named Forest Biotechnologist of the Year

  

  Cary, N.C., February 8, 2012 — Jerry Tuskan, Oak Ridge National Laboratory Distinguished Scientist in the BioSciences Division, has been named 2012 Forest Biotechnologist of the Year by the Institute of Forest Biotechnology (IFB).

  His peers within the Forest Biotechnology Partnership, an international group of forestry and biotechnology professionals, selected Tuskan as the fourth scientist to win this award, which recognizes the forest biotechnologist who best exemplifies responsible uses of forest biotechnology and actively promotes science, dialogue and stewardship through their work. Read more...

• Plant Systems Biology May Newsletter

  

  Contents:

  New ORNL greenhouse completion, Students receive college degrees, ORNL plant scientists develop improved approach for mapping QTL, Kalluri participates in two neutron sciences proposals, Lasers used to study plant-microbe interactions, Students involved in all phases of ORNL plant science research, Wullschleger explores ecosystem warming in the Arctic, and Kalluri attends conference on biofuels.

• Improved Approach for Mapping QTL in a pseudo-Testcross

  

  In this study, an intercross model that incorporates the high heterozygosity and phase uncertainty of outcrossing species was used to reanalyze a published data set on QTL mapping in poplar trees. Several intercross QTLs that are heterozygous in both parents were detected, which are responsible not only for biomass traits, but also for their genetic correlations. This study provides a more complete identification of QTLs responsible for economically important biomass traits in poplars.

  Contributing Authors: Song Wu, Jie Yang, Youjun Huang, Yao Li, Tongming Yin, Stan D. Wullschleger, Gerald A. Tuskan and Rongling Wu

• benefits of LIBS in detection of Endophyte-mediated accumulation of metals

  

  Madhavi Martin's latest article in Journal of Applied Optics shows the benefits of using LIBS to determine the impact of endophyte infection on elemental composition of tall fescue (Festuca arundinacea). Leaf material from both endophyte-infected and endophyte-free tall fescue populations in established plots were examined using ICP MS and LIBS. Seven of eleven metals (Ca, Mg, Fe, Mn, Cu, Ni and Zn) were measured by both techniques at high enough concentrations for reliable comparison, yet levels of Cd were readily detected by LIBS but were below levels typically achieved by ICP MS.

• New greenhouses on the horizon

  

  Construction will soon be finished on three new greenhouses and available for use by ORNL scientists. The greenhouses will almost double bench space for plant and ecosystem science activities. A headhouse for plant and soil processing is also part of the construction package. The greenhouses will be completed early this summer. View the progress.

• Plant Systems Biology March 2010 Newsletter

• Martin's SSSAJ Article Featured in April Edition of CSA News

  

  CSA News’ April edition features an article on Madhavi Martin’s research published in the Soil Science Society of America Journal 2010 January - February issue on using laser-induced breakdown spectroscopy (LIBS) to measure soil carbon. Accurate measurement of soil C will help determine the best “agricultural practices that provide maximum benefits to farmers and the climate alike.”

• ESD researchers contribute to Brachypodium sequencing project

  

  An article describing the sequencing and analysis of the Brachypodium genome was published last week in Nature. Co-authors of the article include the Environmental Sciences Division's Jerry Tuskan, Udaya Kalluri, and Xiaohan Yang.

• Best Poster Award for Laboratory Directed R&D

  

  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., Labbé, 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).

• PSB group intern's poster selected to attend 2009 SERCh

  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

• Gene Expression Profiling Article in Global Change Biology

  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.

• Engle Receives 2008 Technical Support Award in ESD

  

  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.

• Researchers Discover Primer to Plant Defense System

  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.

• Kalluri Receives 24th Annual YWCA Tribute to Women Award

  

  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)

• Yang Receives 2007 Distinguished Achievement Award

  

  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

  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

• Gunter Receives 2007 ESD Technical Support Award

  

  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

  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.