Corn’s Root Evolution Unveiled: Ancient DNA and Modeling Reveal 10,000 Years of Adaptation
Corn, scientifically known as Zea mays, stands today as one of the world’s most extensively cultivated crops, central to global agriculture and food security. Its domestication from the wild grass ancestor teosinte in central Mexico approximately 9,000 years ago marked a transformative event, reshaping its physical and genetic characteristics to meet human needs. While the evolution of corn’s aboveground traits—such as kernel size and ear formation—has been well documented, a recent groundbreaking study led by researchers at Penn State University has delved into the underground world of corn roots to trace their evolutionary journey over the past ten millennia. This investigation integrates ancient DNA analysis, paleobotanical data, and advanced computational modeling to shed light on how root traits adapted in response to environmental shifts and human agricultural practices.
Roots, though hidden beneath the soil, orchestrate a plant’s capacity to acquire water and nutrients and respond to environmental stress. Their role is especially critical under shifting climate conditions, yet their evolutionary trajectory during domestication remains less understood. The Penn State-led team aimed to decode this subterranean legacy by examining genetic material retrieved from ancient corn specimens together with fossilized plant remnants and chemical traces embedded in soil layers. These multidisciplinary data sets were synthesized using OpenSimRoot, a sophisticated computer simulation platform designed to model root architecture and function in varying soil contexts. OpenSimRoot, developed within Penn State’s College of Agricultural Sciences, enables researchers to predict how different root phenotypes influence resource uptake and plant performance.
The study’s findings reveal three profound alterations in corn root architecture that distinguish it from its ancestor teosinte. First, there is a marked reduction in the number of nodal roots, which are roots emerging from the stem base that typically exploit shallow soil horizons. Second, corn roots evolved to develop multiseriate cortical sclerenchyma (MCS), a specialized tissue composed of thick-walled cells that reinforce root strength and facilitate penetration into deeper, often drier soils. This trait had been previously identified by Penn State scientists as beneficial for root depth and drought resistance. Third, the number of seminal roots—those that form early during seed germination and support initial seedling growth—increased, enhancing the plant’s early access to nutrients and water.
To contextualize these morphological changes, the researchers reconstructed environmental conditions of the Tehuacán Valley, a key site of early corn domestication, spanning 18,000 years. They pinpointed fluctuations in atmospheric carbon dioxide concentrations and trace shifts in soil nutrient distributions that influenced root evolution. Between 12,000 and 8,000 years ago, rising CO₂ levels favored the development of deeper root systems, aligning with the emergence of MCS and a reduction in nodal root proliferation. Around 6,000 years ago, the advent of irrigation practices altered nitrogen dynamics, decreasing its availability near the surface and increasing its presence in subsoil layers. This prompted further decline in nodal roots and augmented the functional importance of MCS in accessing nitrogen-rich deeper soils. Subsequently, by approximately 3,500 years ago, an increase in seminal roots coincided with intensified agricultural activity, population growth, and subsequent soil degradation, emphasizing the critical role of early root development in seedling establishment under stressed soil conditions.
Lead author Ivan Lopez-Valdivia, who recently completed his doctoral studies in Plant Science at Penn State, emphasized the study’s innovative integration of ancient genetic data with modeling techniques. This multidisciplinary approach enabled the team to simulate root growth dynamics over millennia, capturing evolutionary responses to both natural environmental variability and anthropogenic influences. Senior author Jonathan Lynch, a distinguished professor and renowned expert in plant nutrition, highlighted the adaptive significance of root traits that mitigate nitrogen stress, underscoring their role in optimizing resource acquisition amid changing agricultural landscapes.
Beyond unraveling the historical trajectory of corn domestication, the insights gained bear profound implications for modern agriculture, particularly in the face of global climate change. Increasing atmospheric CO₂ levels and altered soil nutrient profiles continue to challenge crop productivity worldwide. The study’s revelation that corn roots evolved specific traits to cope with past environmental stresses suggests pathways to engineer or select for root architectures better suited to future conditions. Enhanced deep-root penetration and increased seminal root development may confer resilience against drought and poor soil fertility, essential traits for sustaining yields in a warming, resource-limited world.
The research effort also exemplifies the power of combining paleobotanical records with genetic analysis and computational modeling to dissect plant evolutionary processes. By drawing from a rich assembly of collaborators across multiple disciplines and international institutions, the study leveraged expertise in plant physiology, genetics, archaeology, and computational biology. Co-researchers from institutions including the Swedish University of Agricultural Sciences, the University of Illinois, the University of British Columbia, and the Leibniz Institute of Plant Genetics contributed to a holistic understanding of root trait evolution.
Funding support for this integrative project was provided by multiple agencies, including the Foundation for Food and Agriculture Research, the U.S. Department of Agriculture’s National Institute of Food and Agriculture, the National Science Foundation, Canada’s Social Sciences and Humanities Research Council, and the European Union’s Horizon 2020 framework. This diverse backing underscores the global importance of advancing crop science to meet the challenges of sustainable food production.
Ultimately, this study reframes our understanding of domestication by elevating the role of belowground traits alongside well-studied aboveground characteristics. As Lynch remarked, deciphering the evolutionary pressures that shaped corn’s root systems not only illuminates the past but charts a course for developing crops that can thrive in tomorrow’s changing environments. This research represents a pivotal step toward breeding root systems optimized for efficiency and resilience, ensuring that corn—an ancient staple with deep historical roots—continues to nourish billions in an era of unprecedented ecological change.
Subject of Research: Evolution of corn root traits during domestication
Article Title: Evolution of Corn Root Architecture Traced Through Ancient DNA and Functional-Structural Modeling
Web References:
- OpenSimRoot Model: https://plantscience.psu.edu/research/labs/roots/methods/computer-analysis-tools/simroot
- New Phytologist article DOI: http://dx.doi.org/10.1111/nph.70245
References:
Lopez-Valdivia, I., Sawers, R., Vallebueno-Estrada, M., Rangarajan, H., Swarts, K., Benz, B., Blake, M., Sidhu, J.S., Perez-Limon, S., Schneider, H., & Lynch, J.P. (2024). Evolution of root traits during corn domestication in response to environmental and agricultural changes. New Phytologist. https://doi.org/10.1111/nph.70245
Image Credits: Penn State
Keywords: Agriculture, Crop Domestication, Root Architecture, Corn, Ancient DNA, Plant Evolution, OpenSimRoot, Functional-Structural Modeling, Nitrogen Stress, Climate Adaptation
