Rising sea levels, drought, and excessive groundwater extraction are contributing to soil salinization. Salt stress hampers plant growth, decreases nutrient absorption, and significantly lowers crop yields. A new plant model will assist researchers in identifying genes to improve tolerance to develop more salt-tolerant plants.
A plant’s reaction to stress is governed by the activation of genes, producing RNA copies known as transcripts. These transcripts contain the instructions for generating proteins. Proteins, particularly enzymes, catalyze biochemical reactions to produce metabolites. The resulting proteins and metabolites help protect the plant from salt stress.
Understanding the connection between the expression levels of transcripts from salt-responsive genes, the abundance and activity of metabolites and proteins, and the rate of metabolite reactions (flux) and the resulting phenotypic traits provide valuable insights for identifying gene targets to enhance resilience to salinization.
This insight is not easy to come by. There are about 27,000 protein-coding genes encoding around 35,000 proteins and 8,000 metabolites in Arabidopsis thaliana, a widely used model plant. Connecting those genes, transcripts, proteins and metabolites, and their interactions, together seems impossible. However, this is possible with the use of Genome-scale Metabolic Models (GEMs). GEMs are a mathematical representation of an organism’s metabolism, incorporating data from genomic studies. These models can predict how genetic or environmental changes affect an organism’s metabolism.
Lohani Esterhuizen, a graduate student at the University of Nebraska-Lincoln, developed the first model that links genes and metabolites in roots. The AraRoot model is capable of comprehensively capturing the biomass formation and stress response of the Arabidopsis root system.
“Our AraRoot model represents the first genome-scale metabolic model specifically developed for the Arabidopsis root system. It marks a significant advancement in understanding how plants respond to salt stress—a growing concern as rising sea levels and drought threaten over a billion hectares of arable land worldwide. Previous research into salt tolerance primarily relied on approaches such as genome-wide association studies. However, a comprehensive model of root metabolism had not been developed, largely due to the inherent complexity of root tissues—such as the cortex and endodermis—which vary widely in function and structure,” explains Lohani.
Genome-wide association studies (GWAS) examine correlations between the presence of genetic variants and specific traits, identifying associations without directly assessing gene function. GWAS relies on genetic variants, including mutations, single nucleotide polymorphisms (SNPs), and other genetic differences, to identify associations with traits. In contrast, genome-scale metabolic models focus on gene activation and the biochemical reactions that occur, providing insights into how these reactions contribute to phenotypes. By comparing plants with the same genetic background under different treatments, for example normal growth conditions and stress-induced growth conditions, researchers can identify genes of interest.
“Constructing the AraRoot model involved mapping 2,682 metabolic reactions and 1,310 genes, a task made challenging by the scarcity of root-specific data. To overcome this, we integrated curated information from databases such as KEGG and TAIR into AraRoot and employed computational tools like COBRApy and metabolic bottleneck analysis (MBA).”
The use of MBA allowed the authors to identify 158 genes critical to core metabolic pathways under salt stress. This information can help researchers focus their efforts on genes that would be most likely to lead to improvement in tolerance to high salt environments.
Developing AraRoot for understanding the effect of salt stress on Arabidopsis is only the first step. According to Lohani, “These insights provide a powerful foundation for engineering salt-tolerant crops such as rice or wheat—an essential step toward securing food production in saline environments. Our model can also be adapted to study other stresses like drought, opening doors for undergrads to explore how computational biology can tackle real-world challenges.”
READ THE ARTICLE:
Lohani Esterhuizen, Nicholas Ampimah, Marna D Yandeau-Nelson, Basil J Nikolau, Erin E Sparks, Rajib Saha, AraRoot – A Comprehensive Genome-Scale Metabolic Model for the Arabidopsis Root System, in silico Plants, 2025;, diaf003, https://doi.org/10.1093/insilicoplants/diaf003
AraRoot is freely available on the SSBio GitHub page.
Cover: Image from the article Study Finds Sea-level Rise Is Swallowing Farms in Maryland, Delaware and Virginia Published in Maryland Today that shows stunted corn struggling to grow in a section of a field damaged by saltwater intrusion. It highlights UMD researchers and colleagues studying the phenomenon linked to climate change in the Maryland, Delaware and Virginia portions of the Delmarva Peninsula. Read the associated article titled The spread and cost of saltwater intrusion in the US Mid-Atlantic by Mondal and colleagues. Photo by Becky Epanchin-Niell.
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