Group leader: Luis Oñate-Sánchez - Associate Professor
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Crop production depends primarily on seed vigor, which relates to fast seed germination and robust seedling establishment under a fluctuating environment. The ability of a seed to germinate rapidly and in the right season is of vital importance from an ecological and economical point of view. After germination, the seedling undergoes a transition phase in which the change from heterotrophic to autotrophic growth is key for the establishment of the seedling and its survival. Due to the fragility of these early growth stages, their swiftness and resilience will affect later developmental stages and crop yield. Gibberellins (GAs) are plant hormones with a central role in the processes that determine seed vigor and are required for normal vegetative and reproductive growth.


In order to understand how plants integrate environmental information into growth programs, our group have been studying seed vigor traits and the molecular mechanisms underlying responses to GAs. Results obtained by studying the model plant Arabidopsis thaliana have guided our efforts to translate this knowledge to Brassica and tomato plants with the aim to improve crop performance. To achieve our goals, we have put in place several complementary strategies and a broad set of state-of-the art methods and new techniques developed in our lab. In the last few years, we have identified different molecular mechanisms that regulate seed vigor, specifically dormancy and germination, providing important conceptual insights into the biomechanics of these traits. More recently, we have discovered a novel molecular mechanism mediating nutrient stress responses during and upon seedling establishment with a high biotechnological potential to bolster crop tolerance to stresses.




  1. Tissue-specific mechanisms coordinating seed germination and dormancy.

From a mechanistic point of view, seed germination results from a balance between a physical restriction imposed by the embryo-surrounding tissues (endosperm and testa) and the ability of the embryo to grow and protrude.


We have found that GA-signalling in the Arabidopsis embryo epidermis (along the embryonic axis) is required for proper germination and that the underlying molecular mechanism is coordinating growth of the epidermis with that of inner tissues. This mechanism seems to be controlling cotton fibre cell elongation (Shan et al., 2014), indicating that it has been recruited by other developmental processes and suggesting that it is highly conserved in plants.


Figure 1. The ATML1 and PDF2 genes (left; mRNA in situ hybridization with a PDF2 probe) are specifically expressed in the embryo epidermis and interact with DELLA proteins. According with our results, we have proposed a regulatory model for GA-regulated embryo growth during seed germination (Rombolá-Caldentety et al., 2014).


Trying to understand the relationship between embryo growth and endosperm functionality, we discovered that endosperm cells expand to accommodate embryo growth prior to germination. This process is crucial for germination and two transcription factors (TFs; NAC25 and NAC1L) play pivotal roles in this process by upregulating gene expression of cell-wall remodelling enzymes (CWREs). 


Figure 2. Measuring cell expansion by confocal imaging and 3D geometry reconstruction (left) and regulatory model for GA-mediated endosperm cell expansion critical for germination control (Sánchez-Montesino et al., 2019).


Seed dormancy is a trait that governs the temporal distribution of germination and bestows an evolutionary advantage. It prevents germination in the wrong season, even if short spells of favorable conditions occur. By screening a seed library (Weiste et al., 2007) we have identified a novel TF that links dormancy to germination through feedback and direct regulatory mechanisms. Our results provide genetic and molecular evidence demonstrating the impact of this TF on the activity of important regulators as a relevant mechanism to fine-tune seed dormancy and germination.


  1. Seedling establishment under nutrient imbalance.

Plant growth and development must be coordinated with nutrient availability. Carbon (C) and nitrogen (N) are the two most abundant elements in plant cells, being N the main limiting element in most agricultural soils. Use of fertilizers to increase N availability has a negative economic impact on crop yield and also affect human and environmental wellbeing. High C/N ratios have a negative impact on plant development, including the phase transition from heterotrophic to autotrophic growth crucial for seedling establishment and plant survival. Only a few genes involved in C/N stress responses have been described via genetic analyses.


An initial approach using hormone treatments of plants coupled with confocal microscopy and protein interaction analyses, provided us with enough evidence to unmask a new membrane-associated mechanism able to counteract high C/N stress. Ongoing research is unravelling the full potential of this mechanism to enhance stress tolerance as well as shedding valuable light to design precision breeding and/or biotechnological tools.


Figure 3. Bimolecular fluorescence complementation showing the interaction of proteins of interest (A and B) in membranes of Nicotiana cells. Interaction brings both halves of the GFP protein in close proximity, thus reconstituting the ability to emit green fluorescence. PIP2A is a membrane protein fused to a red fluorescent protein (mCherry). Both signals, green and red colocalized when images (panels 1 and 2) were merged.




  1. Towards improving vigor, growth and stress tolerance in crops

In collaboration with Dr. Mónica Pernas (CBGP), we have carried out physiological, genetic and molecular studies of seed germination in Brassica napus (oilseed rape) and found conservation of regulatory networks previously identified in Arabidopsis. Moreover, we have found that warm temperatures modify transcriptional kinetics associated to germination, thus, having an impact on seedling establishment. Genome edition of specific genes identified by our analyses have rendered plants with altered germination, pointing to them as good targets for breeding or biotechnological approaches to improve stress tolerance in crops.


Figure 4. A) B. napus accessions show variability on seed germination kinetics. Visual differences in a germination time-course between accessions with different germination rates (high, medium, or low; C129, C033, and C032). B) Temporal dynamics of transcriptional changes associated with seed germination uncovered crucial differences at 12 hai between accessions (Boter et al., 2019). C) Extreme germination phenotype in B.napus with a specific regulatory gene edited by CRISPR/Cas9 technology.


Additionally, in the context of C/N responses, we have found a tomato mutant with reduced sensitivity to this nutrient stress that is allowing us to evaluate the conservation of the response studied in Arabidopsis.


Finally, in most tree-breeding programs, the main objective is to increase the level of biomass and abiotic stress resistance. We are using populus as a model tree, in collaboration with Dr. Luis Gómez (CBDS/ETSIMFMN), to study the relationship between GA-promoted growth and stress tolerance observed in herbaceous plants. We are carrying out phenotypic and molecular analyses of transgenic hybrid poplars engineered to modify GA levels to evaluate them as a potential biotechnological tool.



2023-2026 Exploring signalling interactions associated to a novel DELLA degradation mechanism: a new strategy for improving nutrient imbalance in crops. MICINN (PID2022-142059OB-I00). PI: Luis Oñate-Sánchez and Mónica Pernas.

2021-2025: Hormonal coordination between plant growth and nutrients assimilation in response to temperature (Programa Severo Ochoa SEV-2016-0672-20-3; PRE2020-096169). PI: Luis Oñate-Sánchez.

2020-2023: Using gibberellin pathway components to improve crop seed vigour and growth. MICINN (PID2019-109154RB-I00). PIs: Luis Oñate-Sánchez and Luis Gómez.

2021-2023: Improving crop protection and yield using microalgae-derived natural compounds. Doctorado industrial Comunidad de Madrid (IND2020-BIO17311). PI: Luis Oñate Sánchez.

2018-2021: Improving seed vigour in Brassica crops. (Programa Severo Ochoa SEV-2016-0672-20-3; EoI-TSP2-05). PI: Luis Oñate-Sánchez.


Representative Publications

Carrera-Castaño, G., Mira, S., Fañanás-Pueyo, I., Sánchez-Montesino, R., Contreras, Á., Weiste, C., Dröge-Laser, W., Gómez, L., Oñate-Sánchez, L. 2024. Complex control of seed germination timing by ERF50 involves RGL2 antagonism and negative feedback regulation of DOG1. New Phytologist. DOI: 10.1111/nph.19681

Pirredda, M., Fañanás-Pueyo, I., Oñate-Sánchez, L., Mira, S. 2024. Seed Longevity and Ageing: A Review on Physiological and Genetic Factors with an Emphasis on Hormonal Regulation. Plants 13, 41. DOI: 10.3390/plants13010041

Oñate-Sánchez, L., Verdonk, J.C. 2021. Citrate-Citric Acid RNA Isolation (CiAR) for Fast, Low-Cost, and Reliable RNA Extraction from Multiple Plant Species and Tissues. Current Protocols 1, e298. DOI: 10.1002/cpz1.298

Contreras, Á., Merino, I., Álvarez, E., Bolonio, D., Ortiz, J.-E., Oñate-Sánchez, L., Gómez, L. 2021. A poplar short-chain dehydrogenase reductase plays a potential key role in biphenyl detoxification. Proceedings of the National Academy of Sciences USA 118, e2103378118. DOI: 10.1073/pnas.2103378118

Calleja-Cabrera, J., Boter, M., Oñate-Sánchez, L., Pernas, M. 2020. Root Growth Adaptation to Climate Change in Crops. Frontiers in Plant Science 11, 544. DOI: 10.3389/fpls.2020.00544

Carrera-Castaño, G., Calleja-Cabrera, J., Pernas, M., Gómez, L., Oñate-Sánchez, L. 2020. An Updated Overview on the Regulation of Seed Germination. Plants 9, 703. DOI: 10.3390/plants9060703

Boter, M., Calleja-Cabrera, J., Carrera-Castaño, G., Wagner, G., Hatzig, S.V., Snowdon, R.J., Legoahec, L., Bianchetti, G., Bouchereau, A., Nesi, N., Pernas, M., Oñate-Sánchez, L. 2019. An Integrative Approach to Analyze Seed Germination in Brassica napus. Frontiers in Plant Science 10. DOI: 10.3389/fpls.2019.01342

Sánchez-Montesino, R.; Bouza-Morcillo, L.; Marquez, J.; Ghita, M.; Duran-Nebreda, S.; Gómez, L.; Holdsworth, M.J.; Bassel, G.; Oñate-Sánchez, L. 2019. "A regulatory module controlling GA-mediated endosperm cell expansion is critical for seed germination in Arabidopsis". Molecular Plant. DOI: 10.1016/j.molp.2018.10.009.

Gomez, L., Contreras, A., Bolonio, D., Quintana, J., Oñate-Sanchez, L., Merino, I. 2019. Phytoremediation with trees, in: Advances in Botanical Research. Academic Press. DOI: 10.1016/bs.abr.2018.11.010

Sánchez-Montesino, R; Oñate-Sánchez, L. 2018. "Screening arrayed libraries with DNA and protein baits to identify interacting proteins", p. 131-149. In L. Oñate-Sánchez (ed.), Two-Hybrid Systems: Methods and Protocols. Springer New York, New York, NY. DOI: 10.1007/978-1-4939-7871-7_9".

Sánchez-Montesino, R; Oñate-Sánchez, L. 2017. "Yeast one- and two-hybrid high-throughput screenings using arrayed libraries", p. 47-65. In K. Kaufmann and B. Mueller-Roeber (eds.), Plant Gene Regulatory Networks: Methods and Protocols. Springer New York, New York, NY. DOI: 10.1007/978-1-4939-7125-1_5".

Ballester, P; Navarrete-Gómez, M; Carbonero, P; Oñate-Sánchez, L; Ferrándiz, C. 2015. "Leaf expansion in Arabidopsis is controlled by a TCP-NGA regulatory module likely conserved in distantly related species". Physiologia Plantarum. DOI: 10.1111/ppl.12327".

Thatcher, LF; Kamphuis, LG; Hane, JK; Oñate-Sánchez, L; Singh, KB. 2015. "The Arabidopsis KH-Domain RNA-Binding protein ESR1 functions in components of jasmonate signalling, unlinking growth restraint and resistance to stress". PLoS One. DOI: 10.1371/journal.pone.0126978".

Coego, A; Brizuela, E; Castillejo, P; Ruíz, S; Koncz, C; del Pozo, JC; Piñeiro, M; Jarillo, JA; Paz-Ares, J; León, J; Transplanta Consortium, T. 2014. "The TRANSPLANTA collection of Arabidopsis lines: a resource for functional analysis of transcription factors based on their conditional overexpression". Plant Journal. DOI: 10.1111/tpj.12443".

Rombolá-Caldentey, B; Rueda-Romero, P; Iglesias-Fernández, R; Carbonero, P; Oñate-Sánchez, L. 2014. "Arabidopsis DELLA and two HD-ZIP transcription factors regulate GA signaling in the epidermis through the L1 box cis-element". Plant Cell. DOI: 10.1105/tpc.114.127647".

Marin-de la Rosa, N; Sotillo, B; Miskolczi, P; Gibbs, DJ; Vicente, J; Carbonero, P; Onate-Sanchez, L; Holdsworth, MJ; Bhalerao, R; Alabadi, D; Blazquez, MA. 2014. "Large-scale identification of gibberellin-related transcription factors defines group VII ETHYLENE RESPONSE FACTORS as functional DELLA partners". Plant Physiology. DOI: 10.1104/pp.114.244723".

Iglesias-Fernández, R; Wozny, D; Iriondo-de Hond, M; Oñate-Sánchez, L; Carbonero, P; Barrero-Sicilia, C. 2014. "The AtCathB3 gene, encoding a cathepsin B-like protease, is expressed during germination of Arabidopsis thaliana and transcriptionally repressed by the basic leucine zipper protein GBF1". Journal of Experimental Botany. DOI: 10.1093/jxb/eru055".

Rueda-Romero P, Barrero-Sicilia C, Gómez-Cadenas A, Carbonero P and Oñate-Sánchez L* (2012) Arabidopsis thaliana DOF6 negatively affects germination in non-after-ripened seeds and interacts with TCP14. Journal of Experimental Botany 63: 1937-1949.

Iglesias-Fernández, R; Barrero-Sicilia, C; Carrillo-Barral, N; Oñate-Sánchez, L; Carbonero, P. 2013. "Arabidopsis thaliana bZIP44: a transcription factor affecting seed germination and expression of the mannanase encoding gene AtMAN7". Plant Journal. DOI: 10.1111/tpj.12162".

Castrillo G, Turck F, Leveugle M, Lecharny A, Carbonero P, Coupland G, Paz-Ares J and Oñate-Sánchez L* (2011) Speeding cis-trans regulation discovery by phylogenomic analyses coupled with screenings of an arrayed library of Arabidopsis transcription factors. PLoS ONE 6(6): e21524.

Wehner N, Hartmann L, Ehlert A, Böttner S, Oñate-Sánchez L and Dröge-Laser W (2011) High-throughput protoplast trans activation (PTA) system for the analysis of Arabidopsis transcription factor function. The Plant Journal 68: 560-569.