Organ-level gene-regulatory networks inferred from transcriptomic data reveal context-specific regulation and highlight novel regulators of ripening and ABA-mediated responses in tomato
Year: 2025
Type: article
Abstract: Tomato (Solanum lycopersicum) is a globally important crop, yet the gene-regulatory networks (GRNs) that control its gene expression remain poorly understood. In this study, we constructed GRNs for roots, leaves, flowers, fruits, and seeds by inferring transcription factor (TF)-target interactions from over 10 000 RNA-sequencing libraries using the GENIE3 algorithm. We refined these networks using gene co-expression data and computational predictions of TF binding sites. Our networks confirmed key regulators in important processes, including TOMATO AGAMOUS LIKE 1 and RIPENING INHIBITOR in fruit ripening, and SlABF2, SlABF3, and SlABF5 in abscisic acid (ABA) response in leaves. In addition, we identified novel candidate regulators, including AUXIN RESPONSE FACTOR 2A and ETHYLENE RESPONSE FACTOR E2 in fruit ripening and G-BOX BINDING FACTOR 3 (SlGBF3) in ABA-related and drought pathways. To further validate the GRNs, we performed DNA affinity purification sequencing for SlGBF3 and confirmed the accuracy of our GRN predictions. This study provides a valuable resource for dissecting transcriptional regulation in tomato, with potential applications in crop improvement. The GRNs are publicly accessible through a user-friendly web platform at https://plantaeviz.tomsbiolab.com/tomviz.
Source: Plant Communications
Institutions: Universidad Mayor, Millennium Institute for Integrative Biology, Agencia Nacional de Investigación y Desarrollo, Universitat de València, Institute for Integrative Systems Biology, Universidad Andrés Bello, Millennium Science Initiative, University of O'Higgins, Austral University of Chile
Language: English
Subfield: Plant Science
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $3,500
Funders: Ministerio de Ciencia, Innovación y Universidades, Agenția Națională pentru Cercetare și Dezvoltare, European Commission, Generalitat Valenciana, Ministerio de Ciencia e Innovación, Agencia Nacional de Investigación y Desarrollo, European Regional Development Fund, Agencia Estatal de Investigación
Awards: G1098294640, G1171165830, G1453138094, G1527626597, G1708605062, G1773654064, UNRAVELLING THE MECHANISMS CONTROLLING THE TRADE-OFF BETWEEN KERNEL WEIGHT AND GRAIN NUMBER TO IMPROVE YIELD AND CROP ADAPTATION OF WHEAT, G2782794750, MILLENIUM NUCLEUS IN DATA SCIENCE FOR PLANT RESILIENCE, G3279376532, G392015036, G3963198292, IDENTIFYING KEY TRANSCRIPTION FACTORS AND THE DYNAMIC TRANSCRIPTIONAL LOGIC TO ENHANCE DROUGHT TOLERANCE AND GROWTH IN TOMATOES., G4830446884, G5099039979, G5284675477, G5359289489, RESILOMICSNET ESTABLECIMIENTO DE UNA ALIANZA INTERNACIONAL PARA POTENCIAR LA RESILIENCIA CLIMATICA DE ESPECIES DE INTERES PRODUCTIVO, G5423120872, G5603956265, MODELING OF EPIGENETIC GENE REGULATORY NETWORKS IN SWEET CHERRY FLORAL BUDS IN RESPONSE TO DIFFERENTIAL SEASONAL CLIMATE CONDITIONS, GENE REGULATORY CIRCUITRY CONTROLLING DYNAMIC PLANT RESPONSES TO DROUGHT, G629029552, G6488553235, G6629453775, UNRAVELING THE TANLP5 REGULATORY NETWORK UNDER SULFUR DEFICIENCY FOR IMPROVING NUTRIENT USE EFFICIENCY AND GRAIN YIELD IN WHEAT, G7009731043, G7123149454, G713401243, ROLE OF THE SLEIL3 TRANSCRIPTION FACTOR IN THE SULFATE DEFICIENCY RESPONSE OF SOLANUM LYCOPERSICUM., G7434936867, G7559899507, G7696279958, G7726111094, G8070636774, EPIGENETIC CONTROL OF SULFATE-STARVATION RESPONSIVE GENES IN SOLANUM LYCOPERSICUM, G8627105715, G8674105759, G8789181137
OpenAlex ID: W4413963044