agave in green house Sphagnum journal cover Eucalyptus globulus secretory cell in leaf

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, Eucalyptus, Agave, Switchgrass, and Brachypodium), to annuals (Arabidopsis) and Sphagnum 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. the Joint Genome Institute, Pacific Northwest National Lab, Brookhaven National Lab and National Renewable Energy Laboratory) and other academic institutions.

Group News & Updates:

ORNL researchers identify genes best suited for producing biofuel from poplar trees planted in different environments

February 16, 2015. Wellington Muchero discusses the findings of a paper published online in BMC Genomics in the ORNL News article Sugar and Splice.

Wellington Muchero-Exploring poplar gene for biofuel production-YouTube

Genetics: Local climates shaped black cottonwood tree genes

August 25, 2014. The genes associated with climate-driven evolution of the black cottonwood tree are reported in a paper published online this week in Nature Genetics.The results may help conservation efforts for natural populations of plant species in the face of global climate change.

Chrissy Keuper of WUOT speaks with Jerry Tuskan about terpenes from eucalyptus plants

July 25, 2014 Listen

ORNL researchers participate in 34th New Phytologist Symposium in Lake Tahoe

Lake Tahoe, 15-18 July 2014. Oak Ridge National Laboratory researcher Xiaohan Yang heads organizing committee and is joined by others involved in the Engineering CAM Photosynthetic Machinery into Bioenergy Crops for Biofuels Production in Marginal Environments project for a community-wide discussion of Systems Biology and Ecology of CAM plants. See photos from the symposium on Facebook and find details of the program from the New Phytologist website.

Jerry Tuskan named ORNL Corporate Fellow

Tuskan Corporate Fellow

Oak Ridge,TN, June 23, 2014 — Jerry Tuskan, Oak Ridge National Laboratory Distinguished Scientist in the BioSciences Division, has been named a 2014 Corporate Fellow by UT-Battelle. His research focuses on the genetic basis of tree growth and development including collaborations on the genome sequences of poplar and, more recently, eucalyptus biofeedstocks. In 2012, he was the fourth award recipient of the Institute of Forest Biotechnology's Forest Biotechnologist of the Year.

Jerry received his bachelor's degree in forest management from Northern Arizona University, master's in forest genetics from Mississippi State University and doctorate in genetics from Texas A&M University. He has written over 154 journal articles with 7,975 citations.

Jerry Tuskan on eucalyptus-YouTube

Publications - 2015

Davison BH, Brandt CC, Guss AM, Kalluri UC, Palumbo AV, Stouder RL, Webb EG. The impact of biotechnological advances on the future of US bioenergy. Article published online 14 MAY 2015. doi:10.1002/bbb.1549.

Muchero W, Guo J, DiFazio SP, Chen JG, Ranjan P, Slavov GT, Gunter LE, Jawdy SS, Bryan AC, Sykes R, Ziebell A, Kláp T J, Porth I, Skyba O, Unda F, El-Kassaby YA, Douglas CJ, Mansfield SD, Martin J, Schackwitz W, Evans LM, Czarnecki O, Tuskan GA. 2015. High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus. BMC Genomics. 2015 Jan 23;16(1):24. doi:10.1186/s12864-015-1215-z.

Publications - 2014

Borland AM, Wullschleger SD, Weston DJ, Hartwell J, Tuskan GA, Yang X and Cushman JC. 2014. Climate-resilient agroforestry: physiological responses to climate change and engineering of crassulacean acid metabolism (CAM) as a mitigation strategy. Plant, Cell & Environment. doi: 10.1111/pce.12479.

Kalluri UC, Yin H, Yang X and Davison BH, “Systems and synthetic biology approaches to alter plant cell walls and reduce biomass recalcitrance”. Plant Biotechnol J. 2014 Dec;12(9):1207-16.doi: 10.1111/pbi.12283.

Weston DJ, Timm CM, Walker AP, Gu L, Muchero W, Schmutz J, Shaw AJ, Tuskan GA, Warren JM, Wullschleger SD. 2014. Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host–microbiome interactions on understanding ecosystem function. Plant, Cell & Environment. doi/10.1111/pce.12458.

Payyavula RS, Tschaplinski TJ, Jawdy SS, Sykes RW, Tuskan GA, Kalluri UC. Metabolic profiling reveals altered sugar and secondary metabolism in response to UGPase overexpression in Populus. BMC Plant Biology 2014. 14:265.doi:10.1186/s12870-014-0265-8..

Labbé JL, Weston DJ, Dunkirk N, Pelletier DA, Tuskan GA. 2014. Newly identified helper bacteria stimulate ectomycorrhizal formation in Populus. FRONTIERS IN PLANT SCIENCE 5 doi: 10.3389/fpls.2014.00579.

Evans LM, Slavov GT, Rodgers-Melnick E, Martin J, Ranjan P, Muchero W, Brunner AM, Schackwitz W, Gunter LE, Chen JG, Tuskan GA, DiFazio SP. 2014. Population genomics of the model tree Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nature Genetics August 25, 2014.[Epub ahead of print].

Czarnecki O, Yang J, Wang X, Wang S, Muchero W, Tuskan GA, Chen JG. 2014. Characterization of MORE AXILLARY GROWTH Genes in Populus. PLoS One. 2014 Jul 18;9(7):e102757. doi: 10.1371/journal.pone.0102757. eCollection 2014.

Dai X, Hu Q, Cai Q, Feng K, Ye N, Tuskan GA, Milne R, Chen Y, Wan Z, Wang Z, Luo W, Wang K, Wan D, Wang 1, Wang J, Liu J, Yin, T. 2014. The willow genome and divergent evolution from poplar after the common genome duplication. Cell Res. 2014 Jul 1. doi: 10.1038/cr.2014.83. [Epub ahead of print]

Myburg AA, Grattapaglia D, Tuskan GA, et al.. The Genome of Eucalyptus grandis. Nature 2014 11 June. doi:10.1038/nature13308.

Bonito G, Reynolds H, Robeson MS 2nd, Nelson J, Hodkinson BP, Tuskan G, Schadt CW, Vilgalys R.2014. Plant host and soil origin influence fungal and bacterial assemblages in the roots of woody plants. Mol Ecol. 2014 Jul;23(13):3356-70. doi: 10.1111/mec.12821.

Ragauskas AJ, Beckham GT, Biddy MJ, Chandra R, Chen F, Davis MF, Davison BH, Dixon RA, Gilna P, Keller M, Langan P, Naskar AK, Saddler JN, Tschaplinski TJ, Tuskan GA, Wyman CE. Lignin Valorization: Improving Lignin Processing in the Biorefinery. Science 16 May 2014: 1246843 doi:10.1126/science.1246843.

Szövényi P, Devos N, Weston DJ, Yang X, Hock Z, Shaw JA, Shimizu KK, McDaniel SF, Wagner A. Efficient Purging of Deleterious Mutations in Plants with Haploid Selfing Genome Biol Evol 2014 Vol. 6 1238-1252, first published online May 14, 2014. doi:10.1093/gbe/evu099.

Wang SC, Li EY, Porth I, Chen JG, Mansfield SD, Douglas CJ. 2014. Regulation of secondary cell wall biosynthesis by poplar R2R3 MYB transcription factor PtrMYB152 in Arabidopsis. SCIENTIFIC REPORTS 4 DOI: 10.1038/srep05054 Published: MAY 23 2014.

Wang SC, Chen JG. 2014. Regulation of cell fate determination by single-repeat R3 MYB transcription factors in Arabidopsis. FRONTIERS IN PLANT SCIENCE 5 doi: 10.3389/fpls.2014.00133.

McKown AD, Klápště J, Guy RD, Geraldes A, Porth I, Hannemann J, Friedmann M, Muchero W, Tuskan GA, Ehlting J, Cronk QCB, El-Kassaby YA, Mansfield SD, Douglas CJ. 2014. Genome-wide association implicates numerous genes underlying ecological trait variation in natural populations of Populus trichocarpa. New Phytologist, 203: 535–553. doi: 10.1111/nph.12815.

Yin H, Chen CJ, Yang J, Weston DJ, Chen JG, Muchero W, Ye N, Tschaplinski TJ, Wullschleger SD, Cheng ZM, Tuskan GA, Yang X. 2014. Functional Genomics of Drought Tolerance in Bioenergy Crops. Critical Reviews in Plant Sciences 33:205–224 doi: 10.1080/07352689.2014.870417.

Li Z, Czarnecki O, Chourey K, Yang J, Tuskan GA, Hurst GB, Pan C, Chen JG. Strigolactone-Regulated Proteins Revealed by iTRAQ-Based Quantitative Proteomics in Arabidopsis.J Proteome Res. 2014 Mar 7;13 (3):1359-72. doi: 10.1021/pr400925t. Epub 2014 Feb 24.

De Paoli HC, Borland AM, Tuskan GA, Cushman JC, Yang X. 2014. Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities. J Exp Bot. 2014 Feb 24. doi: 10.1093/jxb/eru038.

Tschaplinski TJ, Plett JM, Engle NL, Deveau A, Cushman KC, Martin MZ, Doktycz MJ, Tuskan GA, Brun A, Kohler A, Martin F. 2014. Populus trichocarpa and Populus deltoides exhibit different metabolomic responses to colonization by the symbiotic fungus Laccaria bicolor. Mol Plant Microbe Interact. 2014 Jun;27(6):546-56. doi: 10.1094/MPMI-09-13-0286-R.

Borland AM, Hartwell J, Weston DJ, Schlauch KA, Tschaplinski TJ, Tuskan GA, Yang X, Cushman JC. Engineering crassulacean acid metabolism to improve water-use efficiency.2014. Trends Plant Sci. 2014 Feb 19. pii: S1360-1385(14)00021-1. doi: 10.1016/j.tplants.2014.01.006. [Epub ahead of print] Review.

Deveau A, Gross H, Morin E, Karpinets T, Utturkar S, Mehnaz S, Martin F, Frey-Klett P, Labbé J. 2014. Genome Sequence of the Mycorrhizal Helper Bacterium Pseudomonas fluorescens BBc6R8.Genome Announc. 2014 Jan 9;2(1). pii: e01152-13. doi: 10.1128/genomeA.01152-13.

Muchero W, Labbé J, Ranjan P, DiFazio SP, Tuskan GA. 2014. Genome Resequencing in Populus: Revealing Large-Scale Genome Variation and Implications on Specialized-Trait Genomics. In Challenges and Opportunities for the World's Forests in the 21st Century (pp. 587-595). Springer Netherlands. ISBN 978-94-007-7076-8.

Publications - 2013

Borland AM,Yang X. 2013. Informing the improvement and biodesign of crassulacean acid metabolism via system dynamics modelling. New Phytol. 2013 Dec;200(4):946-9. doi: 10.1111/nph.12529.

Tisserant E, et al. 2013. Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis. Proc Natl Acad Sci U S A. 2013 Dec 10;110(50):20117-22. doi: 10.1073/pnas.1313452110. Epub 2013 Nov 25.

Ma T, et al. 2013. Genomic insights into salt adaptation in a desert poplar. Nat Commun. 2013;4:2797. doi: 10.1038/ncomms3797.

Busby PE, Zimmerman N, Weston DJ, Jawdy SS, Houbraken J, Newcombe G. 2013. Leaf endophytes and Populus genotype affect severity of damage from the necrotrophic leaf pathogen Drepanopeziza populi. ECOSPHERE 4 (10): doi: 10.1890/ES13-00127.1.

Shakya M, Gottel N, Castro Het al. 2013. A multifactor analysis of fungal and bacterial community structure of the root microbiome of mature Populus deltoides trees. 2013. PLoS ONE 8 (10): e76382.doi:10.1371/journal.pone.0076382.

Weston DJ, Wullschleger SD, Tuskan GA. 2013. Extending the Arabidopsis flowering paradigm to a mass flowering phenomenon in the tropics. Mol Ecol. 2013 Sep;22(18):4603-5.doi: 10.1111/mec.12473.

Liu SD, Wang XP, Li EY, Douglas CJ, Chen JG, Wang SC. 2013. R2R3 MYB transcription factor PtrMYB192 regulates flowering time in Arabidopsis by activating FLOWERING LOCUS C. JOURNAL OF PLANT BIOLOGY 56 (4):243-250 doi: 10.1007/s12374-013-0135-1.

Porth I, Klapšte J, Skyba O, Hannemann J, McKown AD, Guy RD, DiFazio SP, Muchero W, Ranjan P, Tuskan GA, Friedmann MC, Ehlting J, Cronk QC, El-Kassaby YA, Douglas CJ, Mansfield SD. 2013. Genome-wide association mapping for wood characteristics in Populus identifies an array of candidate single nucleotide polymorphisms.New Phytol. Nov;200(3):710-26. doi: 10.1111/nph.12422. Epub 2013 Jul 26.

Abraham P, Adams RM, Tuskan GA, Hettich RL. 2013. Moving away from the reference genome: evaluating a peptide sequencing tagging approach for single amino acid polymorphism identifications in the genus Populus. J Proteome Res. 2013 Aug 2;12(8):3642-51. doi: 10.1021/pr400192r. Epub 2013 Jul 23..

Muchero W, Roberts PA, Diop NN, Drabo I, Cisse N, Close TJ, Muranaka S, Boukar O, Ehlers JD. 2013. Genetic architecture of delayed senescence, biomass, and grain yield under drought stress in cowpea. PLoS One. 2013 Jul 30;8(7):e70041. doi: 10.1371/journal.pone.0070041 .

Warren JM, Iversen CM, Garten CT Jr, Norby RJ, Childs J, Brice D, Evans RM, Gu L, Thornton P, Weston DJ. 2013.Timing and magnitude of C partitioning through a young loblolly pine (Pinus taeda L.) stand using 13C labeling and shade treatments. Tree Physiol. 2012 Jun;32(6):799-813. doi: 10.1093/treephys/tpr129. Epub 2011 Dec 30.

Wullschleger SD, Weston DJ. 2013. Modeling the molecular and climatic controls on flowering. New Phytol. 2012 May;194(3):599-601. doi: 10.1111/j.1469-8137.2012.04142.x.

Jin Z, Muchero W, Chen JG. 2013. Analysis of cell division and cell elongation in the hypocotyls of Arabidopsis heterotrimeric G protein mutants. Methods Mol Biol. 2013;1043:37-43. doi: 10.1007/978-1-62703-532-3_4.

Czarnecki O, Yang J, Weston DJ, Tuskan GA, Chen JG.2013. A dual role of strigolactones in phosphate acquisition and utilization in plants. Int J Mol Sci. 2013 Apr 9;14(4):7681-701. doi: 10.3390/ijms14047681.

Urano D, Chen JG, Botella JR, Jones AM. 2013. Heterotrimeric G protein signalling in the plant kingdom. OPEN BIOLOGY 3 Article Number: 120186 DOI: 10.1098/rsob.120186.

Muchero W, Sewell MM, Ranjan P, Gunter LE, Tschaplinski TJ, Yin, T, Tuskan GA. Genome anchored QTLs for biomass productivity in hybrid Populus grown under contrasting environments.PLoS One. 2013;8(1):e54468. doi: 10.1371/journal.pone.0054468. Epub 2013 Jan 29.

Geraldes A, et al. 2013. A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species. Mol Ecol Resour. 2013 Mar;13(2):306-23. doi: 10.1111/1755-0998.12056.

Porth I, Klápště J, Skyba O, Lai BSK, Geraldes A, Muchero W, Tuskan GA, Douglas CJ, El-Kassaby YA, Mansfield SD. 2013. Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations. New Phytologist 197(3):777–790.doi: 10.1111/nph.12014.

Ye CY, Li T, Yin H, Weston DJ, Tuskan GA, Tschaplinski TJ, Yang X. 2013. Evolutionary analyses of non-family genes in plants. Plant J. 73(5):788-97. doi: 10.1111/tpj.12073.

Sukumar P, Legué V, Vayssières A, Martin F, Tuskan GA, Kalluri UC. 2013. Involvement of auxin pathways in modulating root architecture during beneficial plant-microorganism interactions.Plant Cell Environ 36(5):909-19. doi: 10.1111/pce.12036. Review.