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Dr. C.J. Tsai

Winfred N. "Hank" Haynes Professor
Georgia Research Alliance Eminent Scholar

I am a plant biologist with a special passion for large organisms - trees!  Trees are ‘large' not merely by their physical or genome size, but primarily by their longevity.  Longevity depends on a perennial growth habit, which can mean added functionalities for genes, proteins and metabolites compared to herbaceous annuals.  The quest for 'what makes a tree a tree' has led to various projects ranging from gene family evolution and functional diversification, to transgenic manipulation of traits important to growth and development.  Needless to say, our research has industrial relevance due to the importance of forest trees as renewable feedstock.  Our work is also of ecological relevance, because many of the traits we investigate are important in tree interactions with herbivores and pathogens.

We use a variety of experimental approaches in our investigations, ranging from transcriptomics (RNA-Seq, sRNA-Seq and degradome), metabolomics (GC-MS and HPLC-MS) and CRISPR genome editing, to the more traditional tools of genetics, biochemistry and plant physiology.  We accept technical challenges, and have many times developed or adapted necessary tools to advance our research.  For this reason, our lab regularly hosts visiting scholars for technical training, such as insitu hybridization, transcriptomic and metabolomic analysis.

Current Graduate Students:
Ing-Gin Chen (Ph.D.), Forest Biology
Yen-Ho Chen (Ph.D.), Plant Biology
Chen Hsieh (Ph.D.), Bioinformatics
Samantha Surber (Ph.D.), Plant Biology
Trevor Tuma (Ph.D.), Plant Biology

Research Staff:
Patrick Bewg, Postdoctoral Associate
Margot Chen, Research Technician II
Batbayar (Baggi) Nyamdari, Research Professional III
Bindu Simon, Senior Research Associate
Maria Ortega, Senor Research Associate
Alisa Tannirat, Research Professional II
Ran Zhou, Postdoctoral Associate

Selected Publications:

Gu X, Chen I-G, Harding SA, Nyamdari B, Ortega MA, Clermont K, Westwood JH, Tsai C-J (2021) Plasma membrane phylloquinone biosynthesis in nonphotosynthetic parasitic plants. Plant Physiology (2021 Focus Issue on Parasitic Plants). Full text

Tsai C-J (2021) genome editing of woody perennial trees. In: M. Willmann (ed), Genome Editing for Precision Crop breeding. Burleigh Dodds (in press).

Harding SA, Frost CJ, Tsai CJ (2020) Defoliation‐induced compensatory transpiration is compromised in SUT4‐RNAi Populus. Plant Direct 4: 1-13. Full text

Tsai C-J, Xu P, Xue L-J, Hu H, Nyamdari B, Naran R, Zhou X, Goeminne G, Gao R, Gjersing E, Dahlen J, Pattathil S, Hahn MG, Davis MF, Ralph J, Boerjan W, Harding SA (2020) Compensatory guaiacyl lignin biosynthesis at the expense of syringyl lignin in 4CL1-knockout poplar. Plant Physiology 183: 123-136. Full text

Heyduk K, Ray JN, Ayyampalayam S, Moledina N, Borland A, Harding SA, Tsai C-J, Leebens-Mack J (2019) Shared expression of Crassulacean acid metabolism (CAM) genes predates the origin of CAM in the genus YuccaJournal of Experimental Botany 70: 6597-6609. Full text

Ullah C, Tsai C-J, Unsicker S, Xue L-J, Reichelt M, Gershenzon J, Hammerbacher A (2019) Salicylic acid activates poplar defense against the biotrophic rust fungus Melampsora larici-populina via increased accumulation of catechin and proanthocyanidins. New Phytologist. 221: 960-975. Full text 

Harding SA, Tsai CJ (2019) Cell wall pectins in tree growth and woody biomass utilization. In: Canovas FM (ed.), Advances in Botanical Research Vol 89: Molecular Physiology and Biotechnology of Trees. Academic Press, pp. 235-256. 

Bewg WP, Ci D, Tsai C-J (2018) Genome editing in trees: From multiple repair pathways to long-term stability. Frontiers in Plant Science 9:1732.  Full text

Scully E, Geib S, Mason C, Carlson JE, Tien M, Chen H-Y, Harding S, Tsai C-J, Hoover K (2018) Host-plant induced changes in microbial community structure and midgut gene expression in an invasive polyphage (Anoplophora glabripennis). Scientific Reports 8: 9620.  Full text

Tsai CJ, Harding SA, Cooke JEK (2018) Branching out: A new era of investigating physiological processes in forest trees using genomic tools. Tree Physiology 38: 397-408.  Full text

Harding SA, Hu H, Nyamdari B, Xue L-J, Naran R, Tsai C-J (2018) Tubulins, rhythms and cell walls in poplar leaves: it’s all in the timing. Tree Physiology 38: 397-408.  Full text

Hu H, Gu X, Xue L-J, Swamy PS, Harding SA, Tsai C-J (2016) Tubulin C-terminal post-translational modifications do not occur in wood forming tissue of Populus. Frontiers in Plant Science 7, 1493. Full text
Xue L-J, Frost CJ, Tsai C-J, Harding SA (2016) Drought response transcriptomes are altered in poplar with reduced tonoplast sucrose transporter expression. Scientific Reports 6, 33655. Full text

Bowsher AW, Ali R, Harding SA, Tsai C-J, Donovan LA (2016) Evolutionary divergences in root exudate composition among ecologically-contrasting Helianthus species.PLoS One 11: e0148280. Full text

Mason CM, Bowsher AW, Crowell BL, Celoy RM, Tsai C-J, Donovan LA (2016) Macroevolution of leaf defenses and secondary metabolites across the genus HelianthusNew Phytologist 209: 1720-1733Full text

Tsai C-J, Xue L-J (2015) CRISPRing into the woods. GM Crops & Food 6: 206-215. Full text

Bowsher AW, Ali R, Harding SA, Tsai C-J, Donovan LA (2015) Analysis of wild sunflower (Helianthus annuus L.) root exudates using gas chromatography‐mass spectrometry. Journal of Plant Nutrition and Soil Science 178: 776-786. Full text

Swamy PS, Hu H, Pattathil S, Maloney VJ, Xiao H, Xue L-J, Chung J-D, Johnson VE, Zhu Y, Peter GF, Hahn MG,  Mansfield SD, Harding SA, Tsai C-J (2015) Tubulin perturbation leads to unexpected cell wall modifications and affects stomatal behavior in Populus. Journal of Experimental Botany 66: 6507-6518.  Full text

Xue L-J, Alabady MS, Mohebbi M, Tsai C-J (2015) Exploiting genome variation to improve next-generation sequencing data analysis and genome editing efficiency inPopulus tremula x alba 717-1B4.  ree Genetics & Genomes 11: 82. Full text

Xue L-J, Tsai C-J (2015) AGEseq: Analysis of genome editing by sequencing. Molecular Plant 8: 1428-1430. Full text

Zhou X, Jacobs TB, Xue L-J, Harding S, Tsai C-J (2015) Exploiting SNPs for biallelic CRISPR mutations in the outcrossing woody perennial Populus reveals 4-coumrate:CoA ligase specificity and redundancy. New Phytologist 208: 298-301. Full text

Harding SA, Xue L-J, Du L, Nyamdari B, Lindroth RL, Sykes R, Davis MF, Tsai C-J (2014) Condensed tannin biosynthesis and polymerization synergistically condition carbon use, defense, sink strength and growth in PopulusTree Physiology 34: 1240-1251Full text

Peng D, Gu X, Xue L-J, Leebens-Mack JH, Tsai C-J (2014) Bayesian phylogeny of sucrose transporters: Ancient origins, differential expansion and convergent evolution in monocots and dicots.  Frontiers in Plant Science 5: 615.  Full text

Chen H-Y, Babst BA, Nyamdari B, Sykes R, Davis MF, Harding SA, Tsai C-J (2014) Loblolly pine contains phylogenetically divergent 4-coumarate:CoA ligases that confer distinct metabolic phenotypes when over-expressed in PopulusPlant Cell Physiology 55: 1669-1678Full text

Babst BA, Chen H-Y, Wang H-Q, Payyavula RS, Thomas TP, Harding SA, Tsai C-J (2014) Stress responsive Populus hydroxycinnamate glycosyltransferase modulates phenylpropanoid homeostasis.  Journal of Experimental Botany 65: 4191-4200. Full text

da Silva Taveira JH, Borém FM, Figueiredo LP, Reis N, Franca AS, Harding SA, Tsai C-J (2014) Potential markers of coffee genotypes grown in different Brazilian regions: Metabolomics approach. Food Research International 61: 75-82.  Full text

Xu Y, Chen C-F, Thomas TP, Azadi P, Diehl B, Tsai C-J, Brown N, Carlson JE, Tien M, Liang H (2013) Wood chemistry analysis and expression profiling of a poplar clone expressing a tyrosine-rich peptide.  Plant Cell Reports 32: 1827-1841. Abstract

Wang H-Q, Tsai C-J (2013) CorSig: A general framework for estimating statistical significance of correlation and its applciation to gene co-expression analysis.  PLoS ONE 8(10): e77429.  Full text

Xue L-J, Guo W, Yuan Y, Anino EO, Nyamdari B, Wilson MC, Frost CJ, Chen H-Y, Babst BA, Harding SA, Tsai CJ (2013) Constitutively elevated salicylic acid levels alter photosynthesis and oxidative state but not growth in transgenic PopulusPlant Cell 25: 2714-2730.  Full text Image removed.

Tsai C-J (2013) Next-generation sequencing for next-generation breeding, and more.  New Phytologist 198: 635-637.  Full text

Molina-Rueda JJ, Tsai C-J, Kirby EG (2013) The Populus superoxide dismutase gene family and its responses to drought stress in transgenic poplar overexpressing a pine cytosolic glutamine synthetase (GS1a).  PLoS ONE 8(2): e56421.  Full text

Tsai C-J and Harding SA (2013) In situ hybridization.  Methods in Cell Biology 113: 339-359.  Full text

Frost CJ, Nyamdari B, Tsai C-J, Harding SA (2012) The tonoplast-localized sucrose transporter in Populus (PtaSUT4) regulates whole-plant water relations, responses to water stress, and photosynthesis.  PLoS ONE 7(8): e44467.  Full text

Tuominen LK, Johnson VE, Tsai C-J (2011) Differential phylogenetic expansions in BAHD acyltransferases across five angiosperm taxa and evidence of divergent expression among Populus paralogues.  BMC Genomics 12: 236. Full text

Payyavula RS, Tay KHC, Tsai C-J, Harding SA (2011) The sucrose transporter family in Populus: The importance of a tonoplast PtaSUT4 to bioamss and carbon partitioning. Plant Journal 65: 757-770.  Full text Image removed.

Wang H-Q, Tuominen LK, Tsai C-J (2011) SLIM: A sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures. Bioinformatics 27:225-231. Abstract



Schmitz RJ, Zhang X, Tsai CJ, Somatic genetic and epigenetic variations in long-lived perennial trees and their interactions with the environment. NSF Plant Genome Research Program

Leebens-Mack JH, Alabady MS, Tsai C-J, Wadl PA, Xiang J, The dogwood genome project: A model for woody ornamental genomics.  NSF Plant Genome Research Program

Tuskan GA et a., The Center for Bioenergy Innovation. DOE Bioenergy Research Center

Tsai C-J et al., Promoting diversity in agriscience through integrative undergraduate training and research experiences in crop genetics and genomics. USDA-AFRI

Research Areas:

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