Corn root traits evolved with both human-driven, natural environmental changes
Study shows plants adapted to farming and irrigation with root changes that helped corn adjust to low nitrogen and deeper water, making them key to the success of its domestication
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This figure from the paper shows the evolution of root types from teosinte to modern corn over the last 10 000 years, simulated using the modeling program OpenSimRoot, which was developed by scientists in Penn State's College of Agricultural Sciences.
view moreCredit: Penn State
UNIVERSITY PARK, Pa. — Corn was domesticated from its ancestor teosinte in central Mexico beginning about 9,000 years ago by humans selectively breeding the wild plant, transforming its small, hard-shelled kernels into the large, palatable ears of corn we know today. Over the centuries, root traits of corn — now the most widely planted crop in the U.S., and second globally (by acreage) — evolved in response to both changing environmental conditions and human agricultural practices. Because the role of roots in crop domestication in response to shifting circumstances remains unclear — and because it may be relevant to the present when a warming climate is stressing corn and other crops — a team of researchers led by Penn State plant scientists conducted a study to understand how root traits evolved during corn domestication.
The researchers examined DNA from ancient corn plants and analyzed paleobotanical evidence — fossils of ancient plants as well as pollen and chemical signatures — that provide insights into the history of plant life to see how corn roots evolved. They also analyzed how prehistoric atmospheric carbon dioxide levels and human activity influenced these traits. Considering all these factors, they modeled corn root growth and evolution using the OpenSimRoot Model, a computer program designed to simulate crop response to soil conditions, developed in Penn State’s College of Agricultural Sciences. The team recently reported their findings in New Phytologist.
The researchers reported that three major root changes occurred as part of the transformation from teosinte to corn: Fewer nodal roots — shallow roots that grow from the stem base; development of multiseriate cortical sclerenchyma — thick-walled cells in the root that help roots penetrate deeper soils, that was previously discovered by Penn State researchers; and more seminal roots — early-developing roots that help seedlings access nutrients.
“We reconstructed the root phenotypes of corn and teosinte, as well as the environments of the Tehuacán Valley — one of the oldest regions of corn domestication — over the last 18,000 years using a combination of ancient DNA, paleobotany and functional-structural modeling to reconstruct how root traits evolved over time,” said team leader Jonathan Lynch, distinguished professor of plant nutrition, senior author on the study. “The research suggests that root phenotypes that enhance plant performance under nitrogen stress were important for corn adaptation to changing agricultural practices.”
The study traced the following timeline of root trait evolution, according to study first author Ivan Lopez-Valdivia, who earned a doctorate in Plant Science from Penn State in 2024:
— 12,000–8,000 years ago: Carbon dioxide levels rose, favoring deeper root systems. This supported the reduction in nodal roots and appearance of multiseriate cortical sclerenchyma, which help roots grow deeper and access water/nutrients in drier soils.
— By 6,000 years ago: Irrigation was introduced, changing nitrogen availability — less in the topsoil, more in deeper layers. That further reduced nodal roots and presence of multiseriate cortical sclerenchyma became more useful in accessing this subsoil nitrogen.
— Around 3,500 years ago: More seminal roots emerged. Seminal roots are the initial root system that develops from a seed upon germination, playing a crucial role in supporting the seedling’s early growth by absorbing water and nutrients. This coincided with agricultural intensification, population growth and soil degradation — conditions that made early root development more important for survival.
Although the researchers looked far back into time in conducting their study, Lynch suggested the findings may have implications for the future because corn is one of the most important global crops and the climate is changing, with carbon dioxide increasing and soils changing.
“We looked at DNA from ancient corn plant specimens and used environmental data from soil cores that archeologists have generated, put it all together and said, ‘Okay, when corn was originally domesticated, we changed the environment,” he explained. “The amount of carbon dioxide in the atmosphere was changing, and the plant had to develop a different kind of root system. That’s not only interesting historically — because that’s how we got modern corn — but it also gives some guidance as to what we can do with corn roots in the future to make them better adapted to developing conditions.”
Contributing to the research were Ruairidh Sawers, Penn State associate professor of plant response to abiotic stress; Miguel Vallebueno-Estrada, postdoctoral scholar, Swedish University of Agricultural Sciences; Harini Rangarajan, postdoctoral scholar at the University of Illinois; Kelly Swarts, Gregor Mendel Institute of Molecular Plant Biology, Max F. Perutz Laboratories; Bruce Benz, professor of biology, Texas Wesleyan University; Michael Blake, professor and head of the Anthropology Department at the University of British Columbia; Jagdeep Singh Sidhu, former postdoctoral scholar in plant science at Penn State, now assistant professor of crop physiology at South Dakota State University; Sergio Perez-Limon, doctoral candidate in plant science at Penn State; and Hannah Schneider, leader of the Genetics and Physiology of Root Development research group at the Leibniz Institute of Plant Genetics and Crop Plant Research, also a professor at the Georg-August-Universität, Göttingen, Germany.
This project received funding from the Foundation for Food and Agriculture Research, the U.S. Department of Agriculture’s National Institute of Food and Agriculture, the National Science Foundation, the Social Sciences and Humanities Research Council of Canada, and the European Union's Framework Programme for Research and Innovation Horizon 2020.
Journal
New Phytologist
Method of Research
Computational simulation/modeling
Subject of Research
Not applicable
Article Title
In silico analysis of the evolution of root phenotypes during maize domestication in Neolithic soils of Tehuacán
Global team of experts publish guide to elevate plant fluorescence microscopy
Resource aims to boost quality, transparency and reproducibility
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Multi-Color Tobacco
view moreCredit: Donald Danforth Plant Science Center
ST. LOUIS, MO, August 20, 2025 - A team of expert scientists led by Kirk Czymmek, PhD, director of the Advanced Bioimaging Laboratory at the Donald Danforth Plant Science Center and Heather E. McFarlane, assistant professor at the University of Toronto and collaborators from the Danforth Center, University of Leeds (UK), University of Massachusetts (Amherst), University of California - Davis, University of Naples Federico II, University of Minnesota and Université de Montréal, have authored a comprehensive guide to elevate the quality, transparency, and reproducibility of fluorescence microscopy in plant research. The guide was recently published in the journal Plant Cell, “Best Practices in Plant Fluorescence Imaging and Reporting: A Primer”
Microscopy is a fundamental approach used for plant cell and developmental biology as well as an essential tool for mechanistic studies in plant research. However, setting up a new microscopy-based experiment can be challenging, especially for beginner users, when implementing new imaging workflows or when working in an imaging facility where staff may not have extensive experience with plant samples. The basic principles of optics, chemistry, imaging, and data handling are shared among all cell types. However, unique challenges are faced when imaging plant specimens due to their waxy cuticles, strong/broad spectrum autofluorescence, recalcitrant cell walls, and air spaces that impede fixation or live imaging, impacting sample preparation and image quality.
“Our goal was to compile a resource that goes beyond methodological know-how—to elevate competency, transparency and reproducibility in plant imaging across the community,” said Czymmek. “This guide offers plant-specific advice and examples for microscope users at all stages of fluorescence microscopy workflows, from experimental design through sample preparation, image acquisition, processing, and analyses, to image display and methods reporting in manuscripts.”
Topics included:
Addressing Plant-Specific Imaging Challenges:
Fluorescence microscopy in plants faces unique obstacles—waxy cuticles, strong autofluorescence, rigid cell walls, and air-filled tissues can degrade image clarity and impede live imaging.End-to-End Workflow Guidance:
The primer offers thorough recommendations covering experimental design, probe selection, sample prep, imaging modalities, image processing, data handling, quantification, and final reporting—creating a unified workflow framework for all researchers, especially newcomers.Focus on Reproducibility & Reporting Standards:
The authors outline vital metadata disclosure, standards for image display, and guidelines for documenting parameters to support reproducibility and enable future meta-analyses.Illustrative Examples & Tools Provided:
The primer includes practical illustrations—such as comparing widefield, confocal, and super-resolution imaging—and shows protocols to reduce photobleaching, improve signal-to-noise, and manage image compression artifacts, with visual examples demonstrating best vs. suboptimal practices.
The resource, created as part of the National Science Foundation-funded Plant Cell Atlas initiative led by Seung Yon (Sue) Rhee, Director of Michigan State University’s Plant Resilience Institute, provides a baseline standard for plant imaging protocols, enhancing data integrity and enabling researchers across labs to harmonize methodologies. As plant research increasingly relies on complex imaging data, clear best practices are essential for cumulative progress and cross-study comparisons.
“One of the central goals of the Plant Cell Atlas is to empower the plant science community with resources that raise the bar for rigor, transparency, and collaboration. This primer embodies that mission by providing clear, plant-specific guidance for fluorescence microscopy, enabling researchers worldwide to generate high-quality, reproducible data that will accelerate discovery,” said Rhee.
About The Donald Danforth Plant Science Center
Founded in 1998, the Donald Danforth Plant Science Center is a nonprofit research institute with a mission to improve the human condition through plant science. Research, education and outreach aim to have an impact at the nexus of food security and the environment and position the St. Louis region as a world center for plant science. The Center’s work is funded through competitive grants from many sources, including the National Science Foundation, National Institutes of Health, U.S. Department of Energy, the Gates Foundation, and through the support of individuals and corporations.
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For additional information or images please contact: Karla Roeber, kroeber@danforthcenter.org
Journal
The Plant Cell
Article Title
Best practices in plant fluorescence imaging and reporting: A primer
Plant biologist Lucia Strader joins Salk faculty to study plant growth signaling
Salk Institute
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Lucia Strader
view moreCredit: Salk Institute
LA JOLLA (Aug 20, 2025)—The Salk Institute will welcome plant biologist Lucia Strader as a new professor and holder of the Howard H. and Maryam R. Newman Chair in Plant Biology in October 2025. Strader is an internationally recognized leader in plant hormone biology who was previously based at Duke University.
Strader’s lab at Salk will explore how plants sense and integrate environmental cues to shape their growth and development. Her work will advance our fundamental understanding of plant biology and help Salk’s Harnessing Plants Initiative design more resilient crop varieties that can thrive in changing environments.
“Lucia is a world expert in decoding the molecular language plants use to interpret and interact with their environment,” says Salk President Gerald Joyce. “Her innovative, multidisciplinary approach will strengthen Salk’s ongoing efforts to address some of the most pressing agricultural and environmental challenges of our time.”
Humans, like most animals, have very standardized developmental timelines—each transition from infant to child to adult is largely predetermined by our genetic code. But plants are much more flexible. A seed can stay a seed until the conditions are right to sprout; a flower won’t bloom without enough sunlight; a seasonal crop can stay in suspended youth or enter old age with a slight shift in temperature.
At the center of this adaptability is auxin, a hormone that regulates nearly every aspect of plant development—from the timing of leaf growth to the number of petals on a flower. Strader studies how auxin and its molecular partners respond to environmental changes, such as rising temperatures or shifting soil nutrients. Her multidisciplinary approach combines techniques from plant physiology, genetics, molecular biology, biochemistry, structural biology, biophysics, systems biology, and synthetic biology to understand the mechanisms of auxin regulation.
In addition to her ongoing breakthroughs in basic science, Strader is committed to translating this research into field-ready solutions. Her team will use their insights on auxin signaling to engineer plants that can withstand extreme weather, use nutrients more efficiently, and produce reliable yields despite environmental stress. Her findings are already supporting the creation of crops that can pollinate under higher nighttime temperatures and survive with less artificial nitrogen fertilization. The move to Salk will help expand her work in both fundamental and applied research areas.
“Salk has something that can’t be found in other places,” says Strader. “The Institute has a uniquely focused mission that allows its faculty to move science forward with fewer distractions. I’m excited to work with colleagues who share a genuine interest and dedication to pushing the boundaries of knowledge and making a real-world impact.”
Strader studied agronomy at Louisiana State University before earning her PhD in molecular plant sciences at Washington State University and completing her postdoctoral training in biochemistry and cell biology at Rice University. She has received numerous honors, including a fellowship with the American Association for the Advancement of Science and the National Science Foundation’s Early Faculty Career Development Award. She has also been named one of 25 Inspiring Women in Plant Biology by the American Society of Plant Biologists.
About the Salk Institute for Biological Studies:
Unlocking the secrets of life itself is the driving force behind the Salk Institute. Our team of world-class, award-winning scientists pushes the boundaries of knowledge in areas such as neuroscience, cancer research, aging, immunobiology, plant biology, computational biology, and more. Founded by Jonas Salk, developer of the first safe and effective polio vaccine, the Institute is an independent, nonprofit research organization and architectural landmark: small by choice, intimate by nature, and fearless in the face of any challenge. Learn more at www.salk.edu.
Updated lab guide equips researchers with modern tools to identify plant pathogens
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Cover of Laboratory Guide for Identification of Plant Pathogenic Bacteria, Fourth Edition
view moreCredit: © The American Phytopathological Society
A trusted and essential resource for more than four decades, Laboratory Guide for Identification of Plant Pathogenic Bacteria returns in a fully updated fourth edition. This guide remains the most authoritative reference for plant pathologists, diagnosticians, and students who need to accurately identify bacterial plant pathogens using both conventional and cutting-edge methods.
Each chapter is authored by leading experts and provides a holistic, comprehensive overview of the genus or genera, including characteristics useful for identification, isolation techniques, and molecular, serological, biochemical, and other assays for identifying phytobacteria. This updated edition provides simplified identification methods, detailed protocols, color photographs, and a list of semiselective agar media for bacterial isolation. Whether you are an experienced researcher or new to plant pathology, this guide offers the essential tools and knowledge to tackle today’s diagnostic challenges.
This comprehensive volume provides:
- Thorough coverage of more than 30 genera, including 11 not covered in previous editions, such as Dickeya, Lonsdalea, Robbsia, Rhizorhabdus, and Candidatus Liberibacter
- Step-by-step protocols for isolation, culturing, and pathogenicity testing of bacterial strains
- Detailed diagnostic approaches—including molecular, serological, biochemical, and real-time PCR assays—to assist in genus- and species-level identification
- Insightful context on evolving bacterial taxonomy, including the integration of whole genome sequencing and average nucleotide identity in modern species classification
- Two foundational chapters on bacterial taxonomy and initial identification of common genera
Laboratory Guide for Identification of Plant Pathogenic Bacteria, Fourth Edition is dedicated to Norman W. Schaad, the driving force behind the first two editions and lead editor of the third. Schaad was an excellent scientist with a passion for accurate identification of bacterial plant pathogens as well as a friend to many in the field.
This title was published by APS PRESS, the publishing imprint of The American Phytopathological Society, a nonprofit, international organization that advances the science and practice of plant health management in agricultural, urban, and forest settings. The Society was founded in 1908 and has grown from 130 charter members to more than 3,500 scientists and practitioners worldwide.
