State-of-the-art BOOSTER study maps genetic control of maize traits through regulatory DNA variation

The research, titled “Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize,” reveals that genetic differences in regulatory DNA, rather than genes alone, explain most of the heritable diversity observed in maize.​

This international effort involved multiple BOOSTER-affiliated teams, including researchers from Germany, the Netherlands, France, the United States, and China. Together, they constructed the first-ever maize leaf pan-cistrome, a comprehensive map of transcription factor (TF) binding sites, regions of the genome that control gene activity, across 25 diverse maize hybrids grown under both well-watered and drought conditions. By combining cutting-edge genome mapping techniques with advanced bioinformatics, the study identified over 200,000 functional variants that influence how genes are switched on and off, directly linking these variants to differences in plant height, leaf architecture, flowering time, and drought tolerance.

Using an innovative method known as MNase-defined cistrome occupancy analysis (MOA-seq), the team was able to observe how TFs interact with DNA at unprecedented resolution. This approach, developed and refined within the BOOSTER network, allowed researchers to trace how subtle genetic changes impact gene regulation and plant performance. The analysis demonstrated that these regulatory variants, referred to as binding quantitative trait loci (bQTL), account for most of the additive genetic variation in more than 70% of the tested maize traits.

The results also shed new light on how maize responds to drought. Under water-limited conditions, the team discovered more than 14,000 drought-responsive regulatory sites, including regions near genes such as ZmNAC111 and ZmTINY, both associated with drought tolerance. Laboratory validation confirmed that certain drought-tolerant maize lines show stronger activation of these regulatory regions, supporting their potential as targets for future breeding or genome editing.

The study’s success builds on collaborative contributions from several teams, including those at Forschungszentrum Jülich, the Cluster of Excellence on Plant Sciences (CEPLAS), the Max Planck Institute for Plant Breeding Research, Iowa State University, the University of Nebraska–Lincoln, and UC Davis, which together ensured robust data analysis and cross-continental integration of results. Beyond its scientific significance, this achievement illustrates BOOSTER’s capacity to merge genomic science with practical agricultural outcomes. By uncovering how DNA regulatory elements shape plant performance, BOOSTER advances its overarching goal of enabling climate-resilient, data-driven crop improvement. Looking ahead, the consortium plans to expand upon these results by mapping similar regulatory networks across additional tissues and environmental conditions. The data and analytical tools developed are now publicly available, ensuring that breeders and scientists worldwide can access this resource to guide future crop innovations.

Access the full article HERE.

The BOOSTER coordination team congratulates Professor Hartwig and all contributors for this remarkable achievement, which represents a key step toward understanding, and ultimately engineering, the complex genetic networks that sustain agricultural productivity under changing climates.