LA JOLLA (March 19, 2026)—The United States and Mexico have been in a historic megadrought since the turn of the century. For more than 25 years, the American Southwest has faced the severe social and economic consequences of this megadrought—including a $1.1 billion agricultural loss in California in 2021 alone. With these conditions persisting, how can we help crops withstand drought while minimizing yield loss?
Salk Institute scientists profiled nearly a million cells from the leaves of Arabidopsis thaliana, a small flowering plant that serves as a laboratory stand-in for important crops like corn, wheat, and rice. The team measured changes in gene expression in these cells across different drought levels and leaf developmental stages and compiled the data into a public atlas.
The new atlas revealed that drought conditions accelerate leaf aging, but a specific gene could be used to rescue leaf growth during drought.
The study, published in Nature Plants on March 19, 2026, provides a roadmap that could help researchers engineer crop varieties that better maintain growth during drought.
"We have been grinding up leaves and looking at general gene expression for a long time now—this is the first time we are looking at drought with cell type-specific resolution," says Joseph Ecker, PhD, senior author of the study, professor and holder of the Salk International Council Chair in Genetics at Salk, and Howard Hughes Medical Institute Investigator. "We are pushing the boundaries of what is known, and this atlas provides a really critical view into how plants are impacted by their environment."
Do dead leaves make me a bad plant parent?
Plants go through cycles of death and new life, as old leaves fall and new ones bud. This process of aging and development is far more flexible than it is for humans—plants can slow, stop, or speed up aging depending on the situation. For instance, in the face of extreme weather like drought, plants begin to rapidly age and shed older leaves while slowing the growth of new leaves. In doing so, the plant preserves its resources and stays alive.
Unfortunately for farmers, this tactic harms productivity and overall crop yields, resulting in economic losses. And while this stress response, characterized by rapid aging and slowed renewal, is well documented, the genetic underpinnings of leaf growth during drought remain unknown.
"If we can determine how plants fine-tune their growth in response to environmental stress, we can potentially use this information to develop new crop varieties that maintain productivity under water-limited conditions—an increasingly important challenge as droughts become more frequent," says Joseph Swift, PhD, first author of the study and former postdoctoral researcher in Ecker's lab.
What happens inside leaves during drought?
Behind every cell's identity and behavior is a genetic program. There are many genes in each cell, but only a select number are expressed based on that cell type's unique needs. Leaves contain many different specialized cells—ones for transporting water, photosynthesizing, forming the leaf's "skin," and so on. Studies that examine overall gene expression across the entire leaf miss these differences between cell types.
To fix this, the Salk researchers created a gene expression atlas with single-nucleus resolution. The team surveyed 1,226 Arabidopsis leaves, totaling just under one million cell nuclei, including normally grown and watered plants and plants exposed to drought, at various developmental stages.
When the researchers compared the gene expression profiles of all these cells, they found that over the nine-day drought, the leaves accelerated their aging, resulting in smaller leaves. Gene programs related to leaf maturity and aging began activating earlier than normal due to drought stress. The worse the drought conditions, the more intense the expression of aging-related genes.
The aging gene programs were especially pronounced in leaf cells responsible for photosynthesis, called mesophyll cells. They also found specific gene, Ferric Reduction Oxidase 6 (FRO6), was regulating Arabidopsis leaf size during drought.
The team was especially excited to discover that when they increased FRO6 expression in mesophyll cells, the plant partially maintained leaf growth under drought stress.
Could drought-tolerant plants help farmers?
"Usually when we try to engineer drought resistance," explains Swift, "the plant ends up stunted, because you're essentially telling it not to grow. Of course, that isn't what we want out in the field. FRO6 may be a way to encourage plants to keep growing during mild droughts, which would preserve important crop yield for farmers."
These findings have the potential to reshape how crops handle drought, making them more resilient without sacrificing productivity. The findings also complement another recent study from Ecker's lab, which detailed a supercharged immune response that plants initiate post-drought called Drought Recovery-Induced Immunity (DRII).
"Our previous study, published last summer, explained how plants recover from drought, and now we know how they respond during the drought," says Ecker. "From here, we can strategize how to create more robust crops that can better withstand these environmental challenges to protect the global food supply."
Other authors and funding
Other authors include Xuelin Wu, Jiaying Xu, Carl Procko, Tanvi Jain, Natanella Illouz-Eliaz, Joseph Nery, and Joanne Chory of Salk.
The work was supported by the Life Science Research Foundation, American-Australian Association, and Howard Hughes Medical Institute.
About the Salk Institute for Biological Studies
The Salk Institute is an independent, nonprofit research institute founded in 1960 by Jonas Salk, developer of the first safe and effective polio vaccine. The Institute's mission is to drive foundational, collaborative, risk-taking research that addresses society's most pressing challenges, including cancer, Alzheimer's, and agricultural resilience. This foundational science underpins all translational efforts, generating insights that enable new medicines and innovations worldwide. Learn more at www.salk.edu .
