I2SysBio describes the 'internal language of tomato': how its genes communicate to resist drought and improve fruit quality

The Institute of Integrative Systems Biology (I2SysBio), a research center at the University of Valencia Science Park (PCUV), creates a map of tomato metabolism that identifies networks of genes that coordinate the response to water stress and fruit development 

A study by the Institute of Integrative Systems Biology (I2SysBio), joint centre of the Higher Council for Scientific Research (CSIC) and the University of Valencia (UV), located in the scientific-academic area of the University of Valencia Science Park (PCUV); together with Núcleo Milenio Phytolearning (Chile), has deciphered how the genes of tomato (Solanum lycopersicum) communicate with each other to coordinate essential processes such as fruit ripening and drought response. This finding, published in the journal Plant Communications, opens new avenues for developing more resilient and sustainable crops in a context of climate change.

The study, led by I2SysBio researcher Tomás Matus and the directors of Núcleo Milenio Phytolearning, Elena Vidal and José Miguel Álvarez, reveals that the functioning of the tomato plant depends on complex interaction networks, where each organ (roots, leaves, flowers and fruits) organizes its own regulatory strategy.

This work has also generated an authentic 'functional map' of tomato metabolism, identifying the most influential nodes in the network: genes that act as coordinators of the response to water stress (drought) and fruit development

To do this, the team has analysed more than 10,000 sets of gene expression data from different organs and environmental conditions, and reconstructed how genes communicate with each other. "What we finally managed to understand was who gives the orders, who responds and how that conversation changes between a root, a leaf or a fruit," explains Elena Vidal.

This work has also generated a true 'functional map' of tomato metabolism, identifying the most influential nodes in the network: genes that act as coordinators of the response to water stress (drought) and fruit development. "With this information we can design more intelligent genetic improvement strategies, based on complete networks and not isolated hypotheses," says Tomás Matus, co-author of the article and leader of the TomsBio Lab at I2SysBio.

A networked vision for climate change and drought

This research marks a paradigm shift: modifying a single gene can have network-wide effects, requiring strategies based on complete systems. "Adopting a networked vision allows us to understand that in plants there are no genes acting in isolation, but complex communication systems where each gene influences many others," explains Matus.

In contexts such as climate change and drought, this look is key because it helps to discover how plants reorganize their internal networks to adapt to stress: what genes assume leadership roles, how regulatory priorities change between roots, leaves or fruits, and which communication mechanisms are activated or switched off.

"Where crops face increasingly extreme conditions, understanding these networks can help us to anticipate and select varieties with more efficient resilience strategies, instead of focusing on a single 'miracle gene'. It is a more realistic and modern way of understanding plant biology in the face of climate change", Tomas Matus, co-author of the article and TomsBio Lab leader at I2SysBio

"Where crops face increasingly extreme conditions, understanding these networks can help us to anticipate and select varieties with more efficient resilience strategies, rather than focusing on a single 'miracle gene'. It is a more realistic and modern way of understanding plant biology in the face of climate change," says Matus.

TomViz: an open web platform

As part of the study, the team has created TomViz, an interactive platform that allows you to explore tomato gene regulatory networks in a simple and visual way. This tool, integrated into the PlantaeViz environment, offers the scientific community open access to data and functionalities to query genes, identify their connections and generate customized subnets. It also includes options for performing enrichment analysis, visualizing the position of genes in the genome and downloading results in different formats.

Thanks to TomViz, any researcher in Chile, Spain or anywhere else in the world can use this resource to propose new strategies that make crops more drought-resistant, more productive and sustainable, Fostering global collaboration and innovation in genetic improvement.

Don’t miss the intervention of Tomás Matus in Innotransfer 2024 on plant-based industry at PCUV

Source: Delegation CSIC Comunitat Valenciana