How Root Genetics Could Prepare Important Food Crops for a More Extreme Future

2015 Research Team of the McKay Lab (Picture Credit: McKay Lab Website)

On a cool morning in Fort Collins, Colorado, Dr. John McKay walked through rows of maize plants that looked nearly identical–same height, same leaves, same fruit. "Over there, those plants are all the taller ones" he said, pointing to another 15-foot plot of plants with similar heights but taller. Plants in one plot appear so similar but so different across two nearing plots, leaving visitors puzzled and waiting for John’s explanation. But John wasn’t focused on what was above the ground but the hidden architecture below–root systems that determine how plants adapt to prolonged drought, hotter seasons, and other pressures of a warming climate. "Two plants can receive the same amount of water, growing in plots right next to each other, yet behave completely differently," he says, "The reason lies in their genetics."

As climate change accelerates, maize–one of the world's most critical food crops–is facing more threats from heat waves, shifted/irregular precipitation, and declining soil moisture levels. Farmers across the world now face growing uncertainty about whether their fields will produce enough to feed the growing population. Plant biologists like John believe that understanding the genetic basis of resilience is the key for designing crops that can withstand these stresses. The work from John McKay’s lab and collaborators demonstrates how the collaborative efforts involving agricultural workers (for field experiments), data scientists (for genetic analysis), and plant biologists (for functional verification) are charting a path towards a more secure agricultural future.

One of McKay’s most ambitious works is the ROOTS Project, a large collaborative initiative aiming to discover the genetic factors that shape maize root architecture. The goal is to develop plants with deeper, stronger roots – adaptations that can tap into moisture and nutrients deeper under the soil. "Roots are the hidden half of the plant," John explained, "We made progress in building a pipeline to study them at scale." The ROOTS Project brings together field workers, plant geneticists, data scientists, and technicians to build highthroughput genome-scanning pipelines, field-measurement systems, and a large panel of natural maize lines to map rooting depth, mass, and branching patterns. In one example, maize plants were pulled from the ground using a crane-like root-pulling machine (the "Gripper Cage," shown in Figure 1) to measure root-pulling force (RPF)–where higher RPF generally indicates stronger, better-developed roots. Root tissues were then collected to record each plant’s genetic information. Finally, genetic analyses were performed to associate RPF values with specific variants, identifying which genes drive these differences and could serve as targets for future breeding.

Figure 1. Gripper Cage (Left) and Illustration of Root-Pulling: The gripper on the machine grips the maize stalk to pull, where the force and orientation to pull the root out of ground are measured. (Picture Credit: Provided by Dr. John McKay)

The project has already identified promising candidate genes through a genome-wide association study, linking specific genetic variants to root depth, mass and branching patterns (Hein et al., 2025). These candidates are then being tested in mapping populations and functional essays – a critical step called functional verification toward confirming the genes’ roles and integrating them into breeding programs.

But when conversations turn to genetics, especially for food crops, public skepticism often follows. Many people hear the word "genetics" and immediately think of all the down sides of GMOs, almost completely ignoring the fact that how modern agriculture relies on genetic engineering for better crops. I asked McKay how he views these concerns from the public. He paused before answering. "I understand the hesitation. People want transparency in their food. But most of what we do, especially in projects like ROOTS, relies on natural genetic variation already present in maize."–he emphasized that the work is not about inserting foreign genes but understanding and selecting the beneficial ones that maize crops already have or adapt. Still, he believes we must do more than just provide data or results from our work, but also clear explanations and openness.

As droughts intensify across major food crop-growing regions, works to design crops with stronger, deeper roots could help farmers maintain yields during increasingly extreme weather and reduce reliance on irrigation or fertilizer, fundamentally reshaping future agriculture.

Somewhere underground in the roots of the corn, the genes that could feed a warmer world are already growing.