Scientists have developed the first comprehensive genomic atlas of mature plants’ outer protective layer, known as the periderm, along with its carbon-absorbing phellem cells. This research is poised to aid in the creation of stronger plants capable of withstanding climate change.
While plants grow deep into the soil and stretch towards the sunlight, they are fixed in one location and must endure various environmental challenges such as temperature changes, drought, and infections from microbes. To defend against these dangers, many plants have adapted by modifying their structure to form protective layers known as the periderm around their bodies and roots. However, since much of the research in plant biology has focused on younger plants, the later stages of periderm development have not been thoroughly explored.
Researchers at the Salk Institute have unveiled the first detailed gene expression atlas of the plant periderm at a single-cell level. This atlas sheds light on the numerous types of cells within the periderm and identifies the specific genes and biological processes that regulate their development. Notably, the atlas offers valuable insights into phellem cells, which contain suberin—a molecule that helps absorb and store excess carbon from the air over long periods. Scientists can leverage this knowledge to promote the growth of protective periderm in plants under climate-induced stress. Additionally, they may enhance the genes responsible for phellem cell growth to craft plants with superior carbon-capturing and storing capabilities, aligning with Salk’s Harnessing Plants Initiative goals.
The findings were reported in Developmental Cell on January 9, 2025.
“Plants are integral in capturing carbon from the atmosphere and storing it in the ground,” states Professor Wolfgang Busch, the study’s senior author, director of the Harnessing Plants Initiative, and Hess Chair in Plant Science at Salk. “The outer protective layer of plant roots, known as the periderm, consists of various cells that can retain carbon in a durable form. By creating a detailed map of how these root cells develop, we gain a better understanding of how we might enhance this process to help plants retain more carbon in stable forms. This could lead to the development of more resilient plants with stronger roots that contribute to combating climate change.”
Initially, when a plant takes root, it prioritizes primary growth, concentrating on elongating new roots. As it matures, the focus shifts to secondary growth, where the thickening of existing roots occurs alongside the formation of periderm armor. This protective periderm comprises distinct types of cells—phellem, phellogen, and phelloderm—each with unique functions and genetic characteristics that previous studies had not fully explored.
The research team was particularly interested in phellem cells due to their high suberin levels. Suberin is vital to Salk’s Harnessing Plants Initiative, which aims to enhance plants as natural and sustainable methods for capturing carbon. Unlike carbon stored in leaves and stems, which can quickly degrade and re-enter the atmosphere, suberin within plant roots can retain carbon securely in the soil over extended periods. Furthermore, suberin has been shown to increase plants’ resistance to root rot, suggesting it serves a dual purpose of protection and carbon storage.
Earlier studies on the periderm primarily relied on bulk analyses. Although these provided useful information, they lacked specificity regarding different cell types. To overcome this, the Salk team utilized cutting-edge single-cell sequencing techniques to capture unique genetic profiles of each cell type within the periderm. They also monitored changes in gene expression as each cell type developed within the roots of Arabidopsis thaliana—a common model organism in plant research from the mustard family.
“Achieving this level of detail in mature plants over time is unprecedented,” remarks Charlotte Miller, the study’s first author and a research scientist in Busch’s lab. “Previous studies typically ground up entire roots for analysis, but this single-cell approach allows for a deeper understanding of genetic development in each individual cell type of the periderm. This enhanced precision will empower us to engineer stronger, more resilient plants capable of withstanding climate change.”
Using their single-cell time-course sequencing, the researchers discovered that phellem cell development occurs in multiple genetically distinct but interrelated phases. This progressive development was highlighted by key genes like MYB67, which the team found plays a significant role in this process.
By analyzing genetic profiles at various stages of development, the researchers aim to identify specific genes that could stimulate the production of more phellem cells, increase suberin levels, and enhance durable carbon capture capacity.
The periderm atlas also provided significant insights into other non-phellem cells, helping to clarify transitional phases in periderm development—such as how phellogen cells develop into phellem cells. Miller is particularly enthusiastic about further studying these phellogen cells, as their ability to differentiate into diverse cell types late in a plant’s life cycle is intriguing.
Busch is eager to see how suberin-rich cells may fill gaps created by new lateral root growth—a disruptive process where new roots puncture the plant’s surface. Although these responsive suberin-rich cells might not directly form part of the periderm, gaining further insights into periderm cell types and suberin content could enhance understanding of this root branching process and its ability to fend off infections.
“Our research not only pushes the boundaries of plant science but also paves the way for developing stronger crops and improving carbon sequestration through plant roots, addressing both agricultural and climate-related challenges, which is a primary objective of Salk’s Harnessing Plants Initiative,” concludes Busch.
Other collaborators on the study include Sean Jarrell-Hurtado, Manisha Haag, Y. Sara Ye, Mathew Simenc, Paloma Alvarez-Maldonado, Sara Behnami, Ling Zhang, Joseph Swift, Ashot Papikian, Jingting Yu, Kelly Colt, Joseph Ecker, Todd Michael, and Julie Law from Salk.
This research was funded by the Bezos Earth Fund, Hess Corporation, and the TED Audacious Project.
