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, metabolomics 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 in situ hybridization, genome editing, and metabolomic analysis. Current Graduate Students:Chen Hsieh (Ph.D.), BioinformaticsSamantha Surber (Ph.D.), Plant BiologyAudrey Widmier (Ph.D.), Plant BiologyResearch Staff:Cassandra Armstrong, Research TechnicianMargot Chen, Research Professional IMcKenna Coile, Research TechnicianMichihito Deguchi, Postdoctoral AssociateJoe Gauthreaux, Research TechnicianRakesh Loya, Research ProfessionalKimberly McInnes, Research TechnicianBatbayar (Baggi) Nyamdari, Research Professional IIIAitebiremen "Gift" Omokhua-Uyi, Research Professional, Plant Metabolomics LabSaurabh Pandey, Postdoctoral AssociateDipika Parajulee, Research ProfessionalAlisa Tannirat, Research Professional IIDaniela Weber, Research Professional Kangquan Yin, Postdoctoral AssociateRan Zhou, Postdoctoral Associate Awards, Honors and Recognitions: Awards and Honors:2024 IUFRO Working Party 2.04.06 Award for Excellence in Forest Molecular Biology and Genomics (every 2 years)2024 IUFRO Scientific Achievement Award (every 5 years)2022 Member (elected), College of Forest Resources and Environmental Science Honor Academy, MTU2017 Fellow (elected), American Association for the Advancement of Science (AAAS)2013 Fellow (elected), International Academy of Wood Science (IAWS) Research Selected Publications: Deguchi M., Sinclair KM, Patel A, Coile M, Ortega MA, Bewg WP, Tsai C-J (2024) A compendium of nonredundant short Polymerase III promoters for CRISPR applications. bioRxiv 2024.12. 25.630128.Tuma TT, McInnes HA, Pham H, Bewg WP, Surber S, Deguchi M, Zhou R, Lipzen A, Barry KB, Lieb B, Weber Wyneken DL, Harman-Ware AE, Dahlen J, Harding SA, Tsai C-J (2024) CRISPR knockout of winter-biased SUT4 alters phenology, biomass accrual, and fertility of field-grown hybrid poplar. bioRxiv 2024.10.22.619524.Xue L-J, Hozain MI, Frost CJ, Talebi A, Nyamdari B, Aulakh KB, Zhou R, Harding SA, Tsai C-J (2024) Overexpression of plasma membrane SUT1 in poplar alters lateral sucrose partitioning in stem and promotes leaf necrosis. Plant Direct (accepted).Feyissa BA, de Becker EM, Salesse-Smith CE, Zhang J, Yates TB, Xie M, De K, Gotarkar D, Chen MSS, Jawdy SS, Carper DL, Barry K, Schmutz J, Weston DJ, Abraham PE, Tsai C-J, Morrell-Falvey JL, Taylor G, Chen J-G, Tuskan GA, Long SP, Burgess SJ, Muchero W (2024) An orphan gene BOOSTER enhances photosynthetic efficiency and plant productivity. Developmental Cell. Reprint (accepted). Ortega MA, Celoy RM, Chacon F, Yuan Y, Xue L-J, Pandey SP, Drowns MR, Kvitko BH, Tsai C-J (2024) Altering cold-regulated gene expression decouples the salicylic acid–growth tradeoff in Arabidopsis. Plant Cell 36: 4293-4308 (featured story). Reprint Tuma TT, Nyamdari B, Hsieh C, Chen Y-H, Harding SA, Tsai C-J (2024) Perturbation of tonoplast sucrose transport alters carbohydrate utilization for seasonal growth and defense metabolism in coppiced poplar. Tree Physiology 44: tpae061. Reprint Zhou R, Jenkins JW, Zeng Y, Shu S, Jang H, Harding SA, Williams M, Plott C, Barry KW, Koriabine M, Amirebrahimi M, Talag J, Rajasekar S, Grimwood J, Schmitz RJ, Dawe RK, Schmutz J, Tsai C-J (2023) Haplotype-resolved genome assembly of Populus tremula × P. alba reveals aspen-specific megabase satellite DNA. Plant Journal 116: 1003-1017 (cover) Reprint Buell CR, Dardick C, Parrott W, Schmitz RJ, Shih PM, Tsai CJ, Urbanowicz B (2023) Engineering custom morpho- and chemotypes of Populus for sustainable production of biofuels, bioproducts, and biomaterials. Frontiers in Plant Science. 14:1288826. Reprint Yao T, Zhang J, Yates T, Shrestha H, Engle N, Ployet R, John C, Feng K, Bewg WP, Chen MSS, Lu H, Harding SA, Qiao Z, Jawdy S, Shu M, Yuan W, Mozaffari K, Harman-Ware A, Happs R, York L, Binder B, Yoshinaga Y, Daum C, Tschaplinski T, Abraham P, Tsai C-J, Barry K, Lipzen A, Schmutz J, Tuskan G, Chen I-G, Muchero W (2023) eQTL mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus. New Phytologist 239: 2248-2264. Reprint Chen Y-H, Sharma S, Bewg WP, Xue L-J, Gizelbach C, Tsai C-J (2023) Multiplex editing of the Nucleoredoxin1 tandem array in poplar: from small indels to translocations and complex inversions. CRISPR Journal 6: 339-349 (cover). Reprint Brooks EG, Elorriaga E, Liu Y, Duduit JR, Yuan G, Tsai C-J, Tuskan GA, Ranney TG, Yang X, Liu W (2023) Plant promoters and terminators for high-precision bioengineering. BioDesign Research 5: 0013. Reprint Tran S, Ison M, Dias NCF, Ortega MA, Peper A, Hu L, Xu D, Mozaffari K, Chen YFS, Severns PM, Yao Y, Tsai C-J, Teixeira PJPL, Yang L (2023) Endogenous salicylic acid suppresses de novo root regeneration from leaf explants. PLOS Genetics 19(3): e1010636. Reprint Ullah C, Chen Y-H, Ortega MA, Tsai C-J (2023) The diversity of salicylic acid biosynthesis and defense signaling in plants: knowledge gaps and future opportunities. Current Opinion in Plant Biology 72: 102349 (cover). Reprint Ortega MA, Zhou R, Chen MSS, Bewg WP, Simon B, Tsai C-J (2023) In vitro floral development in poplar: insights into seed trichome regulation and trimonoecy. New Phytologist 237: 1078-1081. Reprint Harding SA, Tuma TT, Aulakh K, Ortega MA, Ci D, Ou Y, Tsai C-J (2022) Tonoplast sucrose trafficking modulates starch utilization and water deficit behavior in poplar leaves. Plant Cell Physiology 63: 1117–1129. Reprint Ullah C, Schmidt A, Reichelt M, Tsai C-J, Gershenzon J (2022) Lack of antagonism between salicylic acid and jasmonate signaling pathways in poplar. New Phytologist 235: 701-717. Reprint Bewg WP, Harding SA, Engle N, Vaidya BN, Zhou R, Reeves J, Horn TW, Joshee N, Jenkins J, Shu S, Barry KW, Yoshinaga Y, Grimwood J, Schmitz RJ, Schmutz J, Tschaplinski TJ, Tsai C-J (2022) Multiplex knockout of trichome-regulating MYB duplicates in hybrid poplar using a single gRNA. Plant Physiology 189: 516–526. Reprint Gu X, Chen I-G, Tsai C-J (2021) How do holoparasitic plants exploit vitamin K1? Plant Signaling & Behavior 16: 11. Reprint 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 Science Publishing, Cambridge, UK. 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 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 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 Tsai C-J, Xue L-J (2015) CRISPRing into the woods. GM Crops & Food 6: 206-215. 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 Populus. Tree Physiology 34: 1240-1251. Full 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 Populus. Plant Cell Physiology 55: 1669-1678. Full 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 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 Populus. Plant Cell 25: 2714-2730. Full text Labs/Centers/Committee: Forest Functional Genomics Lab Area of Specialty: Forest Biology Wood Quality Physiology Genetics Biotechnology/Molecular Biology/Genetics Research Areas: Forest Biology Forestry
