A recent study published in Plant Communications has produced detailed maps of gene regulation across different tomato organs, a crop of major national and global importance.
The research was led by José David Fernández, PhD in Integrative Genomics from Universidad Mayor, and involved scientists from the Center for Genomics and Bioinformatics (CGB) at Universidad Mayor, Instituto Milenio iBio, Núcleo Milenio Phytolearning, and the Institute of Integrative Systems Biology (I2SysBio) at the University of Valencia, Spain. The team analyzed data from more than 10,000 gene expression libraries obtained from tomato plants exposed to a wide range of experimental conditions.
Using this extensive dataset, the researchers applied machine-learning algorithms to infer gene regulatory network models. These networks provide a powerful framework for generating hypotheses about how gene expression is controlled and how this regulation underpins organismal function.
The scientists constructed organ-specific gene regulatory networks for five tomato organs — root, leaf, flower, fruit, and seed — and identified key regulatory genes that govern the function of each organ.
The study showed that these networks successfully confirmed the central role of well-known genes involved in fruit ripening and in responses to the plant hormone abscisic acid (ABA). In addition, the analysis uncovered new regulatory candidates with potential key roles in these processes, including SlGBF3, which was experimentally validated as a central regulator of the tomato response to water stress.
An Open Tool
All the gene regulatory networks generated in this study are available on the public platform TomViz, an interactive tool that enables users to explore tomato gene function and regulation and to generate new hypotheses across a wide range of biological contexts, from development to stress responses.
“It’s a very useful tool. When we manage to identify a master regulator — for example, the response to nutrient deficiency or pathogen attack — we can anticipate how the plant will react at the genetic level and design more effective strategies to face stress. This is of high relevance for countries like Chile, where agriculture is one of the main activities, and where climate change imposes important challenges for production,” Fernández explains.
Science with National and International Seal
According to a press release, the article was selected as the cover of the November edition of Plant Communications, highlighting the scientific quality of the research. The illustration was made by biotechnologist Josefa Ormeño, a graduate of the Universidad Mayor in 2025 and a scientific illustrator.
For Fernández, this achievement represents the closure of a key stage of his doctoral training under the mentorship of Dr. Elena Vidal, principal researcher of the CGB, and the beginning of his career as a researcher in genomics and bioinformatics.
“The training provided by the Doctorate in Integrative Genomics allowed me to address problems of high relevance for agricultural productivity through an integrative approach, and train myself in the use of cutting-edge omic and computational tools. Thanks to the support of the University and my tutor, I had the privilege of attending and presenting in relevant scientific meetings in Chile and abroad, in addition to doing an internship in the laboratory of Dr. José Tomás Matus at the I2SysBio in Salamanca, one of the most important Centers in the world in the area of Systems Biology,” Fernández said.
“My doctoral work was part of two publications in prestigious journals in the plant area, in addition to a manuscript that will soon be sent for review. My achievements have allowed me to access a postdoctoral researcher position at the University of Salamanca, so I am very happy and satisfied.”
