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:
New Publication - January 2013
A. Geraldes, S. P. DiFazio, G. T. Slavov, P. Ranjan, W. Muchero, J. Hannemann, L. E. Gunter, A. M. Wymore, C. J. Grassa, N. Farzaneh, I. Porth, A. D. McKown, O. Skyba, E. Li, M. Fujita, J. Klápště, J. Martin, W. Schackwitz, C. Pennacchio, D. Rokhsar, M. C. Friedmann, G. O. Wasteneys, R. D. Guy, Y. A. El-Kassaby, S. D. Mansfield, Q. C. B. Cronk, J. Ehlting, C. J Douglas, G. A. Tuskan. 2013. A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species. Molecular Ecology Resources.
Publication - December 2012
Porth I, Klápště J, Skyba O, Lai BSK, Geraldes A, Muchero W, Tuskan GA, Douglas CJ, El-Kassaby YA, Mansfield SD. 2012. Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations. New Phytologist
Publications - November 2012
Jung, S., Foston, M., Kalluri, U. C., Tuskan, G. A., and A. J. Ragauskas. 2012. 3D chemical image using TOF-SIMS revealing biopolymer component spatial and lateral distributions in biomass. Angew. Chem. Int. Edit. DOI: 10.1002/anie.201205243
Abraham, P., Giannone, R., Adams, R., Kalluri, U., Tuskan, G., and R. Hettich. 2012. Putting the pieces together: High-performance LC-MS/MS provides network-, pathway-, and protein-level perspectives in Populus. Mol. Cell. Proteom. DOI: 10.1074/mcp.M112.022996
Publication - October 2012
Stan D. Wullschleger, D.J. Weston, S.P. DiFazio, and G.A. Tuskan. 2012. Revisiting the sequencing of the first tree genome: Populus trichocarpa. Tree Physiology
Publications - September 2012
Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W, Rodgers-‐Melnick E, Lipphardt MF, Pennacchio CP, Hellsten U, Pennacchio LA, Gunter LE, Ranjan P, Vining K, Pomraning KR, Wilhelm LJ, Pellegrini M, Mockler TC, Freitag M, Geraldes A, El Kassaby YA, Mansfield SD, Cronk QCB, Douglas CJ, Strauss SH, Rokhsar D, Tuskan GA. 2012. Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytologist DOI: 10.1111/j.1469-‐8137.2012.04258.x
Guo, J., Morrell-Falvey, J., Labbé, J., Muchero, W., Kalluri, U., Tuskan, G., and J.-G. Chen. 2012. Highly efficient isolation of Populus mesophyll protoplasts and its application in transient expression assays. PLoS ONE 7: e44908.
Publications - June 2012
Weston DJ, Pelletier DA, Morrell-Falvey JL, Tschaplinski TJ, Jawdy SA, Lu TY, Allen SM, Karve A, Melton SJ, Martin MZ, Schadt CW, Chen JG, Yang X, Doktycz MJ, Tuskan G. 2012. Pseudomonas fluorescens induces strain-dependent and strain-independent host plant responses in defense networks, primary metabolism, photosynthesis and fitness. Molecular Plant-Microbe Interactions, 25: 765-778.
Bennetzen, JL, Schmutz, J, Wang, H, Percifield, R, Hawkins, J, Pontaroli, AC, Estep, M, Feng, L, Vaughn, JN, Grimwood, J, Jenkins, J, Barry, K, Lindquist, E, Hellsten, U, Deshpande, S, Wang, X, Wu, X, Mitros, T, Triplett, J, Yang, X, Ye, CY, Mauro-‐Herrara, M, Wang, L, Li, P, Sharma, M, Sharma, R, Ronald, PC, Panaud, O, Kellogg, EA, Brutnell, T, Doust, A, Tuskan, GA, Rokhsar, D, Devos KM. 2012. Full genome sequence analysis of the model plant Setaria. Nat. Biotech. 30(6):555-‐561.
Publications - May 2012
Induri, BR, Ellis, DR, Slavov, GT, Yin, T, Zhang, X, Muchero, W, Tuskan, GA, DiFazio, SP. 2012. Identification of quantitative trait loci and candidate genes for cadmium tolerance in Populus. Tree Physiol 32(5): 626-‐638.
Publications - March 2012
GA Tuskan, S DiFazio, P Faivre-Rampant, M Gaudet, A Harfouche, V Jorge, JL Labbé, P Ranjan, M Sabatti, G Slavov, N Street, TJ Tschaplinski, T Yin. The obscure events contributing to the evolution of an incipient sex chromosome in Populus: a retrospective working hypothesis (2012) Tree Genome and Genetics: DOI 10.1007/s11295-012-0495-6
Ye, X, S Yuan, H Guo, F Chen, GA Tuskan, Z-‐M Cheng. 2012. Evolution and divergence of the poplar gene family encoding xyloglucan endotransglycosylase/hydrolases in the coding and promoter regions. Tree Genet Genom 8(1):177-‐194.
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...
Publication - February 2012
Tisserant, E, Kohler A, Dozolme-‐Seddas P, Balestrini R, Benabdellah K, Colard A, Croll D, Da Silva C, Gomez SK, Koul R, Ferrol N, Fiorilli V, Formey D, Franken P, Helber N, Hijri M, Lanfranco L, Lindquist E, Liu Y, Malbreil M, Morin E, Poulain J, Shapiro H, van Tuinen D, Waschke A, Azcón-‐Aguilar C, Bécard G, Bonfante P, Harrison MJ, Küster H, Lammers P, Paszkowski U, Requena N, Rensing SA, Roux C, Sanders IR, Shachar-‐Hill Y, Tuskan G, Young JP, Gianinazzi-‐Pearson V, Martin F. 2012. The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional trade offs in an obligate symbiont. New Phyto. 193(3):755-‐ 769.
Publications - January 2012
L Vincenot, K Nara, C Sthultz, J Labbé, MP Dubois, L Tedersoo, F Martin and MA Selosse. Extensive gene flow over Europe and possible speciation over Eurasia in the ectomycorrhizal basidiomycete Laccaria amethystina complex (2012) Molecular Ecology 21(2): 281-299
Abraham, P, Adams, R, Giannone, R, Kalluri, U, Ranjan, P, Erickson, B, Shah, M, Tuskan, G, Hettich, R. 2012. Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics. J Proteome Res 11(1):449-‐460.
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.”
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.
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.
