Discovery Reveals Regulatory DNA as an Underexplored Goldmine for Crop Breeding and Climate Resilience

In a recent Nature Genetics publication, an international team led by Dr. Thomas Hartwig and Dr. Julia Engelhorn (Max Planck Institute for Plant Breeding Research, Cologne; Heinrich Heine University Düsseldorf) introduces a scalable method to map genomic regulatory regions—often referred to as “switches” for their role in controlling the timing and strength of gene expression. Until now, most research has focused on genes themselves, but this study demonstrates that many crucial trait differences originate from variation in these regulatory switches, which have long been notoriously difficult to study on a large scale.

Natural genetic variation drives biodiversity and evolution—but adapting crops to today’s rapidly shifting climate cannot wait the millennia that evolution typically demands. To safeguard global food security, researchers must urgently identify DNA variants that enhance crop performance under stress—starting now.

In a recent Nature Genetics publication, an international team led by Dr. Thomas Hartwig and Dr. Julia Engelhorn (Max Planck Institute for Plant Breeding Research, Cologne; Heinrich Heine University Düsseldorf) introduces a scalable method to map genomic regulatory regions—often referred to as “switches” for their role in controlling the timing and strength of gene expression. Until now, most research has focused on genes themselves, but this study demonstrates that many crucial trait differences originate from variation in these regulatory switches, which have long been notoriously difficult to study on a large scale.

Analyzing 25 diverse maize hybrids, the researchers pinpointed over 200,000 genomic regions where natural variation impacts regulatory switches. These variations significantly influence key agronomic traits such as plant height, leaf morphology, and tolerance to drought and disease.

Remarkably, although these regulatory switches make up less than 1 % of the genome, variation at these sites often explains a substantial share of heritable trait differences—sometimes exceeding half. This discovery offers plant breeders a powerful new avenue: targeting regulatory switches to accelerate the development of climate-resilient varieties.

Dr. Hartwig comments, “Understanding how these regulatory switches operate provides powerful new tools to enhance both crop resilience and yield—laying the foundation for smarter crops in the future.”

The team applied their method specifically to drought stress, identifying over 3,500 individual regulatory switches and their associated genes that respond to water-limited conditions. The precision of this mapping enables targeted manipulation of these switches to develop plants with improved drought resilience.

Dr. Engelhorn adds, “Our hybrid-based assay allows direct comparison of maternal and paternal regulatory alleles in a single experiment. We now offer the research community a resource of over 3,500 drought-linked regulatory sites—opening new possibilities to fine-tune gene expression for enhanced robustness.”

Co-author Samantha Snodgrass (University of California, Davis) underscores the shift in perspective: “Despite decades of revolutionary work on genome evolution, much of the non-coding genome remains a black box. This exciting new method pulls back the curtain—providing breeders and biologists with precise targets in regions previously overlooked.”

The study was supported by a broad range of funding sources, including the CEPLAS Cluster of Excellence on Plant Sciences at HHU—focused on developing ’SMART plants in dynamic environments’—and the European Horizon Europe project BOOSTER, which aims to boost drought resilience in cereals. Additional support came from the German Research Foundation (DFG), the Alexander von Humboldt Foundation, the U.S. National Science Foundation, the U.S. Departments of Agriculture and Energy, the EU’s Seventh Framework Programme, and the Helmholtz Association.