Winfred N. "Hank" Haynes Professor
Georgia Research Alliance Eminent Scholar
Ph.D. (1995) Michigan Technological University

Contact Info
  • Grant Support
    • Dissecting the oxidative stress response regulons of Populus. USDA-AFRI
    • Somatic genetic and epigenetic variations in long-lived perennial trees and their interactions with the environment. NSF (PI, Schmitz) 
    • The dogwood genome project: A model for woody ornamental genomics. NSF (PI, Leebens-Mack) 
    • The Center for Bioenergy Innovation. DOE (PI, Tuskan)
    • The dual effect of tubulin manipulation on Populus wood formation and drought tolerance. DOE
    • A new paradigm of carbohydrate utilization in pollen. USDA-AFRI
  • Research Interests
    • 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. 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. 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.
Selected Publications:
  • Harding SA, Hu H, Nyamdari B, Xue L-J, Naran R, Tsai C-J (2017) Tubulins, rhythms and cell walls in poplar leaves: it’s all in the timing. Tree Physiology (online early).

  • 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 tissues of Populus.  Frontiers in Plant Science 7: 1493.

  • 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.

  • 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.

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

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

  • 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.

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

  • 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. 

  • 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.

  • 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 in Populus tremula x alba 717-1B4.  Tree Genetics and Genomics 11:82. 

  • 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 and growth in Populus.  Tree Physiology 34: 1240-1251.

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

  • 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 Populus. Plant Cell Physiology 55: 1669-1678.

  • 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.

  • 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.

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

  • 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.

  • Xue L-J, Guo W, Yuan Y, Anino EO, Nyamdari B, Wilson MC, Frost CJ, Chen H-Y, Babst BA, Harding SA and Tsai C-J (2013) Constitutively elevated salicylic acid levels alter photosynthesis and oxidative state, but not growth in transgenic Populus.  Plant Cell 25: 2714-2730.  Recommended by Faculty of 1000. 

  • Tsai C-J (2013) Next-generation sequencing for next-generation breeding, and more. New Phytologist 198: 635-637.
  • 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 cystolic glutamine synthase (GS1a). PLoS One 8(2): e56421.

  • Tsai C-J, Harding SA (2013) In situ hybridization. 113: 339-359.

  • Frost CJ, Nyamdari B, Tasi 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.

  • 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.

  • 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. Recommended by Faculty of 1000. 

  • Wang HQ, 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.

  • Wegrzyn JL, Eckert AJ, Choi M, Lee JM, Stanton BJ, Sykes R, Davis MF, Tsai CJ, Neale DB (2010) Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem. New Phytologist 188: 515-532.

  • Gou J, Strauss SH, Tsai C-J, Fang K, Chen Y, Jiang X, Busov VB (2010) Gibberellins regulate lateral root formation in Populus through interaction with auxin and other hormones. Plant Cell 22: 623-639.

  • Babst, B.A., S.A. Harding and C.-J. Tsai. 2010. Biosynthesis of phenolic glycosides from phenylpropanoid and benzenoid precursors in Populus. Journal of Chemical Ecology 36: 286-297.

  • Payyavula, R.S., B.A. Babst, M.P. Nelsen, S.A. Harding and C.-J. Tsai. 2009. Glycosylation-mediated phenylpropanoid partitioning in Populus tremuloides cell cultures. BMC Plant Biology 9: 151.

  • Yuan Y, Chung J-D, Fu X, Johnson VE, Ranjan P, Booth SL, Harding SA, Tsai CJ (2009) Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and Arabidopsis. Proceedings of the National Academy of Sciences USA 106: 22020-22025.

  • Harding SA, Jarvie MM, Lindroth RL, Tsai CJ (2009) A comparative analysis of phenylpropanoid metabolism, N utilization, and carbon partitioning in fast- and slow-growing Populus hybrid clones. Journal of Experimental Botany 60: 3443-3452.

  • Cseke LJ, Tsai C-J, Rogers A, Nelsen MP, White HL, Karnosky DF, Podila GK (2009) Transcriptomic comparison in the leaves of two aspen genotypes having similar carbon assimilation rates but different partitioning patterns under elevated [CO2]. New Phytologist 182: 891-911.

  • Qin H, Feng T, Harding SA, Tsai C-J, Zhang S (2008) An efficient method to identify differentially expressed genes in microarray experiments. Bioinformatics 24: 1583-1589.

  • Luo K, Harding SA, Tsai C-J (2008) A modified T-vector for simplified assembly of hairpin RNAi constructs. Biotechnology Letters 30: 1271-1274.

  • Oakley RV, Wang Y-S, Ramakrishna W, Harding SA, Tsai C-J (2007) Differential expansion and expression of alpha- and beta-tubulin gene families in Populus. Plant Physiology 145: 961-973.

  • Rajinikanth M, Harding SA, Tsai C-J (2007) The glycine decarboxylase complex multienzyme family in Populus. Journal of Experimental Botany 58: 1761-1770.

  • Brodeur-Campbell SE, Vucetich JA, Richter DL, Waite TA, Rosemier JN, Tsai C-J (2006) Insect herbivory on low-lignin transgenic aspen. Environmental Entomology 35: 1696-1701.

  • Tuskan GA et al. (110 authors). (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science 313: 1596-1604.

  • Tsai, C.-J., Harding S.A., Tschaplinski T.J., Lindroth R.L. and Y. Yuan. 2006. Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus. New Phytologist 172: 47-62.

  • Harding SA, Jiang H, Jeong ML, Casado FL, Lin H-W, Tsai C-J (2005) Functional genomics analysis of foliar condensed tannin and phenolic glycoside regulation in natural cottonwood hybrids. Tree Physiology 25: 1475-1486.

  • Jeong ML, Jiang H, Chen H-S, Tsai C-J, Harding SA (2004) Metabolic profiling the sink to source transition in developing leaves of quaking aspen (Populus tremuloides). Plant Physiology 136: 3364-3375.

  • Ranjan P, Kao Y-Y, Jiang H, Joshi CP, Harding SA, Tsai C-J (2004) Suppression subtractive hybridization-mediated transcriptome analysis from multiple tissues of aspen (Populus tremuloides) trees altered in phenylpropanoid metabolism. Planta 219: 694-704.

  • Kao Y-Y, Harding SA, Tsai C-J (2002) Differential expression of two distinct phenylalanine ammonia-lyase genes in condensed tannin-accumulating and lignifying cells of quaking aspen. Plant Physiology 130: 796-807.

  • Harding SA, Leshkevich J, Chiang VL, Tsai C-J (2002) Differential substrate inhibition couples kinetically distinct 4-coumarate:CoA ligases with spatially distinct metabolic roles in quaking aspen. Plant Physiology 128: 428-438.
Of note:
  • Editor, Tree Physiology
  • Review Editor, Frontiers in Plant Biotechnology
  • Fellow, American Association for the Advancement of Science (AAAS)
  • Fellow, International Academy of Wood Science (IAWS)
  • UGA Plant Center Director (2014-2017) 
Personal Website:

Articles Featuring Chung-Jui (CJ) Tsai

Tuesday, March 17, 2015 - 9:54am

Genetics scientist featured in the Columns: "UGA researchers think they've come up with a system to identify the genes in trees responsible for stress tolerance, which includes everything from extreme temperatures to disease.

Monday, March 16, 2015 - 9:14am

Genetics scientist highlighted as Focus on Faculty: CJ Tsai, the Winfred N.

Monday, January 26, 2015 - 3:26pm

Genetics scientist was featured in the Columns:

Senior Vice President for Academic Affairs and Provost Pamela Whitten has appointed a committee to begin a national search to fill the position of dean of the Warnell School of Forestry and Natural Resources.