ADAPTIVE GENETICS AND GENOMICS

Group leader: Jose María Jiménez Gómez - Researcher CSIC
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Personnel:


 

Research overview:

Since their appearance on earth, plants have naturally evolved mechanisms to thrive in every possible ecosystem. Some of the most interesting cases of plant adaptation have occurred during domestication, where humans strongly selected for characteristics of agricultural interest. Understanding the molecular basis of these adaptive mechanisms is one of the mayor quests in modern biology and the goal of the Adaptive Genomics and Genetics group. We believe that knowledge on the genes and proteins responsible for the variation we observe in the world today will help us breed better crops in the future.

The Adaptive Genomics and Genetics group combines expertise in genomics, genetics and molecular biology and works mainly in two model systems: Arabidopsis thaliana and tomato. Arabidopsis is our model to study natural adaptation, because of its worldwide distribution across many different environments, its small genome, ease of growth and its abundant genetic and genomic resources. Tomato is our model for domestication because its importance as food, its relatively small homozygous genome, and its well-studied domestication history.


Research lines:


Circadian rhythms in agriculture


Our lab showed that domestication delayed circadian rhythms in tomato through selection of knockout alleles of EID1 and LNK2, two light signaling genes (Figure 1). Our working hypothesis is that this modification of light signaling and circadian rhythms represent an advantage for tomato under the long days it encountered when it moved out of its equatorial origin. Our lab works now towards demonstrating this hypothesis and towards characterizing the relationship between light signaling, circadian rhythms and plant performance.


Figure 1. Domestication delayed circadian rhythms in tomato. A) Mean relative position of cotyledon tip over time under constant light of 34 cultivated tomato accessions (red) and 44 S. pimpinellifolium accessions (yellow). Colored shading shows SEM; hatched areas in the background indicate subjective nights. Data from 8 independent experiments. B) Mean circadian period and phase estimates ± SEM (n = 2-5) of the genotypes shown in A). C) Genome-wide logarithm of the odds (LOD) scores from a QTL analysis on leaf movements for phase (red ) and period (black) in a S. pimpinellifolium x S. lycopersicum RIL population. The dashed horizontal line indicates the 5 % significance threshold. D) Mean period (left) and phase (right) estimates ± SEM of transgenic lines carrying wild (yellow) or cultivated (red) alleles of LNK2 (left) and EID1 (right). Stars indicate significant differences (one-way ANOVA and post-hoc Tukey’s HSD test, p < 0.01). E) Gene model representations for EID1 and LNK2 indicating the mutations found in cultivated tomato. F) frequency of mutations in EID1 and LNK2 shown in E) among accessions representing several domestication steps from left to right. Number of accessions of each group is indicated on the x axis.
 


Genomics of tomato domestication


Large sets of genomic resources such as resequencing, metabolomics and transcriptomics for cultivated and wild tomato accessions have been made publicly available in the last years (Figure 2). Our lab is using these datasets to investigate the effects of domestication and breeding in the genome of this crop. For example, we collaborate with other groups to study the evolution of transposable elements along tomato domestication or the effect of wild introgressions in the genome of cultivated tomato.


Figure 2. Tomato phylogeny. Neighbor-joining tree of tomato accessions constructed from ~1800 genome-wide SNPs extracted from short read (~700 accessions) and microarray data (~1000 accessions). Color in each accession is determined by its passport data (gold color for accessions of unknown origin). Outside circles were drawn to delimit sensible phylogenetic groups.
 


Arabidopsis natural variation


We have been exploring natural variation in metabolite content and gene expression in Arabidopsis thaliana. This is allowing us to find genes and mutations that change the chemical composition or the regulatory networks of plants adapted to different environments. The figure below shows QTL peaks for 22 metabolites that show variation in a Col x Cvi recombinant inbred line population.


Figure 3. Metabolite QTLs in Arabidopsis. Heatmap of estimated effects from a QTL analysis on 10 metabolites that present the highest variation in a Col-0 x Cvi recombinant inbred line population. Red lines indicate the highest LOD score for each metabolite.

 


Legumes: genetic diversity and molecular bases of drought and salt tolerance

We have been exploring the natural variation of legumes to identify varieties with enhanced drought tolerance and improved nitrogen fixation capacity. We focus on three species: Vicia sativa (common vetch), Cicer arietinum (chickpea), and Lens culinaris (lentil). We rely on the extensive collections of the Spanish Plant Genetic Resources Center (INIA-CSIC), one of the world’s largest genebanks, which plays a critical role in conserving legume diversity and providing novel traits for climate-resilient agriculture. In parallel, we are analyzing the impact of symbiotic interactions with nitrogen-fixing bacteria on stress tolerance. This is being addressed through integrated biochemical, physiological, and transcriptomic approaches to better understand the mechanisms that link symbiosis to stress resilience.


Figure 4. Dual approach to select drought tolerant legume varieties using natural genetic variation from genebanks.

 

Funding
  • PID2021-122138OR-I00 GREVISA: Genetic Resources of Vicia sativa for a Sustainable Agriculture. (01/09/2022 - 31/08/2025). IP: Elena Ramírez-Parra
  • PID2023-151867OB-C33 CLIMVAR: Unlocking the genetic diversity of wild tomato relatives for climate-resilient tomato breeding (01/12/2024 - 01/12/2027). IP: José M Jiménez-Gómez
  • CBGP-CEPLAS TOMATIME: Domestication of the circadian clock in tomato and its effect in light and temperature stress responses (01/04/2024 - 01/04/2027). IP: José M Jiménez-Gómez and K Wabnik
  • PATHFINDER-101098680      Darkwin: Pollinator-assisted plant natural selection and breeding under climate change pressure. (01/01/2023 - 01/06/2026). IP: F Pérez-Alfocea
  • CDTI-IDI-20240292 BIOVID:  Evaluación del genotipado de nueva generación como herramienta para la identificación de biotipos de vid adaptables a variaciones agroclimáticas. (01/04/2024 - 01/04/2026). IP: Viveros Villanueva
  • PTI Agro4Food (CSIC Interdisciplinary Thematic Platform. Recovery of plant genetic biodiversity. Optimization of agricultural and forestry systems). 01/01/2025 - 31/12/2027 AEI, Spain. IP: L. Guasch & R. Malvar
  • SEP-210571680-862862-INCREASE Intelligent Collections of Food Legumes Genetic Resources for European Agrofood Systems 01/09/2020 -31/08/2025. H2020-EU. IP: R. Papa
  • RED2022-134237 (AEI-MICINN) Leguminous Research Network 01/01/2023 - 31/12/2025. AEI, Spain. IP: D. Rubiales
  • Conexion CSIC Recursos Genéticos (REGEN) 2025-2027 IP: P. Revilla D. Grivet

 

 


Representative Publications

Juan-Cabot, A., Carrillo, L., Fullana-Pericàs, M., Galmés, J., Medina, J., Conesa, M.À. 2025. Mediterranean Tomato Landraces Exhibit Genotype-Specific Transcriptomic Responses to Water Stress. Physiologia Plantarum 177, e70696. DOI: 10.1111/ppl.70696

Martínez Rivas, F.J., Wozny, D., Xue, Z., Gilbault, E., Sapir, T., Rouille, M., Ricou, A., Medina, J., Noël, L.D., Lauber, E., Voxeur, A., Mazier, M., Loudet, O., Clément, G., Jiménez-Gómez, J.M. 2025. Parallel evolution of salinity tolerance in Arabidopsis thaliana accessions from Cape Verde Islands. Science Advances 11, eadq8210. DOI: 10.1126/sciadv.adq8210

Contreras-Riquelme, J.S., Contreras, M., Moyano, T.C., Sjoberg, R., Jimenez-Gomez, J., Alvarez, J.M. 2025. Desert-adapted tomato Solanum pennellii exhibit unique regulatory elements and stress-ready transcriptome patterns to drought. PLOS ONE 20, e0324724. DOI: 10.1371/journal.pone.0324724

González-Delgado, A., Martínez-Rivas, F.J., Jiménez-Gómez, J.M. 2025. Photoperiod insensitivity in crops. Journal of Experimental Botany eraf153. DOI: 10.1093/jxb/eraf153

Glaus, A.N., Brechet, M., Swinnen, G., Lebeigle, L., Iwaszkiewicz, J., Ambrosini, G., Julca, I., Zhang, J., Roberts, R., Iseli, C., Guex, N., Jiménez-Gómez, J., Glover, N., Martin, G.B., Strickler, S., Soyk, S. 2025. Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing. Nature Genetics 1–11. DOI: 10.1038/s41588-024-02026-9

Xue, Z., Ferrand, M., Gilbault, E., Zurfluh, O., Clément, G., Marmagne, A., Huguet, S., Jiménez-Gómez, J.M., Krapp, A., Meyer, C., Loudet, O. 2024. Natural variation in response to combined water and nitrogen deficiencies in Arabidopsis. The Plant Cell koae173. DOI: 10.1093/plcell/koae173

Pérez-Alfocea, F., Borghi, M., Guerrero, J.J., Jiménez, A.R., Jiménez-Gómez, J.M., Fernie, A.R., Bartomeus, I. 2024. Pollinator-assisted plant phenotyping, selection, and breeding for crop resilience to abiotic stresses. The Plant Journal. DOI: 10.1111/tpj.16748

Xiang, Y., Sapir, T., Rouillard, P., Ferrand, M., Jiménez-Gómez, J.M. 2022. Interaction between photoperiod and variation in circadian rhythms in tomato. BMC Plant Biology 22, 187. DOI: 10.1186/s12870-022-03565-1

Domínguez, M., Dugas, E., Benchouaia, M., Leduque, B., Jiménez-Gómez, J.M., Colot, V., Quadrana, L. 2020. The impact of transposable elements on tomato diversity. Nature Communications 11, 4058. DOI: 10.1038/s41467-020-17874-2

Zhang, L., Jiménez-Gómez, J.M. 2020. Functional analysis of FRIGIDA using naturally occurring variation in Arabidopsis thaliana. The Plant Journal 103, 154–165. DOI: 10.1111/tpj.14716

Van Dooren, T.J.M., Silveira, A.B., Gilbault, E., Jiménez-Gómez, J.M., Martin, A., Bach, L., Tisné, S., Quadrana, L., Loudet, O., Colot, V. 2020. Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects. Journal of Experimental Botany 71, 3588–3602. DOI: 10.1093/jxb/eraa132

Yuste-Lisbona, F.J., Fernández-Lozano, A., Pineda, B., Bretones, S., Ortíz-Atienza, A., García-Sogo, B., Müller, N.A., Angosto, T., Capel, J., Moreno, V., Jiménez-Gómez, J.M., Lozano, R. 2020. ENO regulates tomato fruit size through the floral meristem development network. Proceedings of the National Academy of Sciences 117, 8187–8195. DOI: 10.1073/pnas.1913688117

Hu, Y., Mesihovic, A., Jiménez-Gómez, J.M., Röth, S., Gebhardt, P., Bublak, D., Bovy, A., Scharf, K.-D., Schleiff, E., Fragkostefanakis, S. 2020. Natural variation in HsfA2 pre-mRNA splicing is associated with changes in thermotolerance during tomato domestication. New Phytologist 225, 1297–1310. DOI: 10.1111/nph.16221

Huertas, R., Catalá, R., Jiménez-Gómez, J.M., Mar Castellano, M., Crevillén, P., Piñeiro, M., Jarillo, J.A., Salinas, J. 2019. Arabidopsis SME1 Regulates Plant Development and Response to Abiotic Stress by Determining Spliceosome Activity Specificity. The Plant Cell 31, 537–554. DOI: 10.1105/tpc.18.00689

Fantini, E., Sulli, M., Zhang, L., Aprea, G., Jiménez-Gómez, J.M., Bendahmane, A., Perrotta, G., Giuliano, G., Facella, P. 2019. Pivotal Roles of Cryptochromes 1a and 2 in Tomato Development and Physiology. Plant Physiology 179, 732–748. DOI: 10.1104/pp.18.00793