Group leader: Isabel Allona Alberich - Professor
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Group leader: Mariano Perales - Assistant Professor
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Isabel Allona


Scopus: 6601911052

Mariano Perales


Scopus: 8622144900

Daniel Conde

Scopus: 55455766600 


Phenology of temperate woody perennials is determined by the environment. Long days and warm temperatures promote growth. Day shortening and a drop of temperatures induce dormancy, but once established, growth cannot resume until a minimal requirement of cold hours has been satisfied. Moreover, tree acclimation to seasons involves the activation of adaptative mechanism related to plant stress tolerance. Understanding woody perennials response to the environment will contribute with an efficient vegetative and reproductive tree growth, reduce economic costs in tree management, and improve productivity, adaptation and geographical distribution.


Poplar is regarded as a model temperate tree species in forest genetics, genomics, physiology and phytoremediation. Poplar (Populus spp.) is a genus of fast growing trees with economic importance for biomass production worldwide. We aim to understand fundamental mechanisms determining environmental control of poplar development for engineering the best climate-smart genetic material to develop plus trees. To achieve that, we are investigating the following processes:




Hypothesis:Periodic genes are the first layer of environmental surveillance that guides plant developmental transitions, growth dynamics, periodic physiology and stress responses

Our Approach
: We investigate the function and molecular mechanism of periodic genes (diurnal and circadian) in poplar tree model. We apply genetics (CRISPR/Cas9), genomics, molecular and cell biology tools, and computational modeling in collaboration with Dr. K. Wabnik laboratory (CBGP, UPM-INIA/CSIC). We focus on poplar homologs to Arabidopsis genes with roles in:


  1. Flowering time regulators
  2. Circadian clock regulators
  3. Light signaling mediators





Hypothesis:It is possible to bioengineer or biostimulate seasonal dormancy break and flowering in perennials


Our Approach: We look for seasonal regulators and metabolites that promote shoot apical meristem growth reactivation. We focus on thermoresponsive genes, proteins, and metabolites obtained through:


  1. Transcriptomic and methylome studies
  2. Proteomic studies
  3. Non targeted metabolomic studies
  4. Chemical screening
  5. Plant phenological and biostimulation assays





Hypothesis:Stress related transcription factors can improve poplar heavy metals phytoextraction from polluted soil


Our Approach: We investigate the phytoextraction potential of poplar overexpressing and knock out lines of stress-related transcription factors. Physiology and genomic of heavy metal accumulation are investigated to understand and improve poplar phytoextraction molecular mechanism. This project is developed in collaboration Dr. Michel Chalot laboratory (UBFC, France) and the bioremediation experts Horizon BIOSYSMO consortium.






Hypothesis:It is possible to bioengineer drought tolerant poplars by manipulating shoot vascular and stomatal development

Our Approach:
We are implementing scRNA-Seq to identify unique cell types, states, and responses on a single- cell level of poplar under well irrigated and severe drought conditions. Using snRNA-seq pipeline, we will define complex regulatory networks that change in response to stress, providing a map to uncover critical mechanisms of cell specific drought stress tolerance in trees.  This work is conducted by Dr. Daniel Conde junior leader La Caixa in CBGP (https://www.cbgp.upm.es/index.php/es/?option=com_content&view=article&id=945) and Dr. Matias Kirst laboratory UF, USA




Hypothesis:Light signaling modulate development of the root system, its function and response to drought


Our Approach: We investigate the effect of the light quality and/or quantity signaling on poplar root system development using root clock luciferase reporter lines. We take advantage of CRISPR mutants of shoot light signaling regulators created in our laboratory to explore the effect on light quality and quantity on root development and function in collaboration with Dr. Moreno-Risueño laboratory (CBGP, UPM-INIA/CSIC).




FRUITFLOW: Predicting and tuning seasonal responses of apple and peach to improve orchard yield and climate change resilience to Mariano Perales. 2021-2024.   ERANET Suscrop 2.


Identifying the molecular regulatory mechanisms of stem cell differentiation during the formation of new organs in trees, by applying single-cell transcriptomics to Daniel Conde. 2023-2026. La Caixa Junior Leader Fellowship Incoming.


MoReGrow: Molecular bases of poplar response to environmental cues and abiotic stresses for maximizing plant growth to Mariano Perales e Isabel Allona. 2022-2025. Proyectos I+D+i -Modalidades «Retos Investigación» y «Generación de Conocimiento». Proyecto PID2021-123060OB-I00 financiado por MCIN/ AEI /10.13039/501100011033/ y por FEDER Una manera de hacer Europa.


BIOSYSMO:Bioremediation Systems Exploiting Synergies for Improved Removal of Mixed Pollutants to Isabel Allona. 2022-2026. Funded by the European Union under the GA no 101060211.



R-C BOOSTS CDR: Secuestro del dióxido de carbono atmosférico en raíces de chopo empleando el reloj de la raíz y aumento del contenido de metabolitos de baja degradación. TED2021-129530B-I00



Representative Publications

Ding, J., Wang, K., Pandey, S., Perales, M., Allona, I., Khan, M.R.I., Busov, V.B., Bhalerao, R.P. 2024. Molecular Advances of Bud Dormancy in Trees. Journal of Experimental Botany erae183. DOI: 10.1093/jxb/erae183

Triozzi, P.M., Brunello, L., Novi, G., Ferri, G., Cardarelli, F., Loreti, E., Perales, M., Perata, P. 2024. Spatiotemporal oxygen dynamics in young leaves reveal cyclic hypoxia in plants. Molecular Plant 17, 377–394. DOI: 10.1016/j.molp.2024.01.006

Alique, D., D., Redondo López, A., González Schain N., ,Allona, I., Wabnik, K., Perales, M. 2024. Core clock genes adjust growth cessation time to day-night switches in poplar. Nature Communications 15, 1784. DOI: 10.1038/s41467-024-46081-6

Perez-Garcia, P., Pucciariello, O., Sanchez-Corrionero, A., Cabrera, J., del Barrio, C., Del Pozo, J.C., Perales, M., Wabnik, K., Moreno-Risueno, M.A. 2023. The cold-induced factor CBF3 mediates root stem cell activity, regeneration and developmental responses to cold. Plant Communications 100737. DOI: 10.1016/j.xplc.2023.100737

Sreedasyam, A., Plott, C., Hossain, M.S., Lovell, J.T., Grimwood, J., Jenkins, J.W., Daum, C., Barry, K., Carlson, J., Shu, S., Phillips, J., Amirebrahimi, M., Zane, M., Wang, M., Goodstein, D., Haas, F.B., Hiss, M., Perroud, P.-F., Jawdy, S.S., Yang, Y., Hu, R., Johnson, J., Kropat, J., Gallaher, S.D., Lipzen, A., Shakirov, E.V., Weng, X., Torres-Jerez, I., Weers, B., Conde, D., Pappas, M.R., Liu, L., Muchlinski, A., Jiang, H., Shyu, C., Huang, P., Sebastian, J., Laiben, C., Medlin, A., Carey, S., Carrell, A.A., Chen, J.-G., Perales, M., Swaminathan, K., Allona, I., Grattapaglia, D., Cooper, E.A., Tholl, D., Vogel, J.P., Weston, D.J., Yang, X., Brutnell, T.P., Kellogg, E.A., Baxter, I., Udvardi, M., Tang, Y., Mockler, T.C., Juenger, T.E., Mullet, J., Rensing, S.A., Tuskan, G.A., Merchant, S.S., Stacey, G., Schmutz, J. 2023. JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom. Nucleic Acids Research 51, 8383–8401. DOI: 10.1093/nar/gkad616

Vigneaud, J., Kohler, A., Sow, M.D., Delaunay, A., Fauchery, L., Guinet, F., Daviaud, C., Barry, K.W., Keymanesh, K., Johnson, J., Singan, V., Grigoriev, I., Fichot, R., Conde, D., Perales, M., Tost, J., Martin, F.M., Allona, I., Strauss, S.H., Veneault-Fourrey, C., Maury, S. 2023. DNA hypomethylation of the host tree impairs interaction with mutualistic ectomycorrhizal fungus. New Phytologist. DOI: 10.1111/nph.18734

Gómez-Soto, D., Allona, I., Perales, M. 2022. FLOWERING LOCUS T2 Promotes Shoot Apex Development and Restricts Internode Elongation via the 13-Hydroxylation Gibberellin Biosynthesis Pathway in Poplar. Frontiers in Plant Science 12. DOI: 10.3389/fpls.2021.814195

Gómez-Soto, D., Ramos-Sánchez, J.M., Alique, D., Conde, D., Triozzi, P.M., Perales, M., Allona, I. 2021. Overexpression of a SOC1-Related Gene Promotes Bud Break in Ecodormant Poplars. Frontiers in Plant Science 12. DOI: 10.3389/fpls.2021.670497

Allona, I., Kirst, M., Boerjan, W., Strauss, S., Sederof, R. (Eds.) 2019. Forest Genomics and Biotechnology. Frontiers in Plant Science. DOI: 10.3389/978-2-88963-178-0

Ramos-Sánchez, J.M., Triozzi, P.M., Alique, D., Geng, F., Gao, M., Jaeger, K.E., Wigge, P.A., Allona, I., Perales, M. 2019. LHY2 Integrates Night-Length Information to Determine Timing of Poplar Photoperiodic Growth. Current Biology. DOI: 10.1016/j.cub.2019.06.003

Conde, D., Perales, M., Sreedasyam, A., Tuskan, G.A., Lloret, A., Badenes, M.L., González-Melendi, P., Ríos, G., Allona, I. 2019. Engineering Tree Seasonal Cycles of Growth Through Chromatin Modification. Frontiers in Plant Science 10. DOI: 10.3389/fpls.2019.00412

Maurya, J.P., Triozzi, P.M., Bhalerao, R.P., Perales, M. 2018. Environmentally Sensitive Molecular Switches Drive Poplar Phenology. Frontiers in Plant Science 9, 1873. DOI: 10.3389/fpls.2018.01873

Sow, M.D., Allona, I., Ambroise, C., Conde, D., Fichot, R., Gribkova, S., Jorge, V., Le-Provost, G., Pâques, L., Plomion, C., Salse, J., Sanchez, L., Segura, V., Tost, J., Maury, S. 2018. Epigenetics in Forest Trees: State of the Art and Potential Implications for Breeding and Management in a Context of Climate Change. Advances in Botanical Research. DOI: 10.1016/bs.abr.2018.09.003

Triozzi, PM; Ramos-Sánchez, JM; Hernández-Verdeja, T; Moreno-Cortés, A; Allona, I; Perales, M. 2018. "Photoperiodic regulation of shoot apical growth in poplar". Frontiers in Plant Science. DOI: 10.3389/fpls.2018.01030".

Conde, D; Moreno-Cortés, A; Dervinis, C; Ramos-Sánchez, JM; Kirst, M; Perales, M; González-Melendi, P; Allona, I. 2017. "Overexpression of DEMETER, a DNA demethylase, promotes early apical bud maturation in poplar". Plant, Cell & Environment. DOI: 10.1111/pce.13056".

Conde, D; Le Gac, A-L; Perales, M; Dervinis, C; Kirst, M; Maury, S; González-Melendi, P; Allona, I. 2017. "Chilling responsive DEMETER-LIKE DNA demethylase mediates in poplar bud break". Plant, Cell & Environment. DOI: 10.1111/pce.13019".

Ramos-Sánchez, JM; Triozzi, PM; Moreno-Cortés, A; Conde, D; Perales, M; Allona, I. 2017. "Real-time monitoring of PtaHMGB activity in poplar transactivation assays". Plant Methods. DOI: 10.1186/s13007-017-0199-x".

Moreno-Cortés, A; Ramos-Sánchez, JM; Hernández-Verdeja, T; González-Melendi, P; Alves, A; Simòes, R; Rodrigues, JC; Guijarro, M; Canellas, I; Sixto, H; Allona, I. 2017. "Impact of RAV1-engineering on poplar biomass production: a short-rotation coppice field trial". Biotechnology for Biofuels. DOI: 10.1186/s13068-017-0795-z".

Corredoira, E; San José, MC; Vieitez, AM; Allona, I; Aragoncillo, C; Ballester, A. 2016. "Agrobacterium-mediated transformation of European chestnut somatic embryos with a Castanea sativa (Mill.) endochitinase gene". New Forests. DOI: 10.1007/s11056-016-9537-5".

Pilate, G; Allona, I; Boerjan, W; Déjardin, A; Fladung, M; Gallardo, F; Häggman, H; Jansson, S; Acker, R; Halpin, C. 2016. "Lessons from 25 Years of GM Tree Field Trials in Europe and Prospects for the Future", p. 67-100. In C. Vettori, F. Gallardo, H. Häggman, V. Kazana, F. Migliacci, G. Pilate, and M. Fladung (eds.), Biosafety of Forest Transgenic Trees: Improving the Scientific Basis for Safe Tree Development and Implementation of EU Policy Directives, vol. 82. Springer Netherlands, Dordrecht. DOI: 10.1007/978-94-017-7531-1_4".

Johansson, M; Ramos-Sánchez, JM; Conde, D; Ibáñez, C; Takata, N; Allona, I; Eriksson, ME. 2015. "Role of the circadian clock in cold acclimation and winter dormancy in perennial plants", p. 51-74. In J. V. Anderson (ed.), Advances in Plant Dormancy. Springer International Publishing.

Ibañez, C; Collada, C; Casado, R; González-Melendi, P; Aragoncillo, C; Allona, I. 2013. "Winter induction of the galactinol synthase gene is associated with endodormancy in chestnut trees". Trees. DOI: 10.1007/s00468-013-0879-8".

Conde, D; González-Melendi, P; Allona, I. 2013. "Poplar stems show opposite epigenetic patterns during winter dormancy and vegetative growth". Trees. DOI: 10.1007/s00468-012-0800-x".

Corredoira, E.; Valladares, S.; Allona, I.; Aragoncillo, C.; Vieitez, A.M.; Ballester, A. 2012. “Genetic transformation of European chestnut somatic embryos with a native thaumatin-like protein (CsTL1) gene isolated from Castanea sativa seeds”. Tree Physiology 32:1389-1402.

Moreno-Cortes, A; Hernandez-Verdeja, T; Sanchez-Jimenez, P; Gonzalez-Melendi, P; Aragoncillo, C; Allona, I. 2012. CsRAV1 induces sylleptic branching in hybrid poplar. New Phytologist 194:83-90.