The scientific foundation of the work is paleogenomics, the reconstruction of genomes that no longer exist. Rather than extracting DNA from fossils, the researchers used computational comparisons of living species to infer the gene content and organization of their long-extinct common ancestors. They analyzed and compared 84 genomes from modern flowering plants chosen to represent cultivated plants around the world. From this comparative dataset, the team reconstructed ten ancestral paleogenomes, effectively a set of founder gene catalogues from which today’s species descend. Because these reconstructions capture the ancestral genomic context of each gene, they allow scientists to identify genes that have kept both their shared ancestral position and their biological function over hundreds of millions of years of evolution.

That combination—conserved genomic context plus conserved function—is what makes the approach so powerful for plant breeding. A gene that has persisted with the same role across multiple species is more likely to drive traits of real agronomic importance, such as tolerance to drought or the timing of flowering, both of which are central to how crops respond to shifting climates. Instead of studying each crop species in isolation, breeders can use these conserved genes as a translational bridge: knowledge of what a gene does in one well-characterized species can be applied to a related crop where the same gene has been detected in its ancestral context.

Beyond its practical implications, the reconstruction of the paleogenomes delivered fundamental insights into the evolutionary history of the plant kingdom. By dating the ancestral genomes, the team was able to establish when the major botanical families emerged, and to retrace key evolutionary trajectories that shaped the diversity of plants we see today. These include the divergences between aquatic and terrestrial plants, between herbaceous and woody species, between C3 and C4 photosynthetic types, and between species that form symbiotic nitrogen-modulating associations and those that do not. Each of these transitions represents a major innovation in plant evolution, and anchoring them in time provides a framework for understanding how plants have repeatedly adapted to new environments.

With this evolutionary map in hand, the researchers turned to wheat and barley, two cereals of exceptional agronomic significance. Both were among the first crops domesticated more than 10,000 years ago in the Fertile Crescent, and both supported the very emergence of agriculture. Their histories run in parallel: similar timelines of domestication, similar environmental conditions, and similar pressures exerted by human selection. That parallel history makes them an ideal natural experiment. If both species, evolving under the same climatic constraints, retained the same adaptive genetic variants, then those variants are strong candidates for genes that confer resilience in Mediterranean and semi-arid environments—the kinds of conditions that climate change is expected to make more common.

To carry out this comparison at scale, the team studied 1,420 modern varieties representing the global genetic diversity of wheat and barley, alongside the remains of ancient wheat dating back 5,000 years. By scanning this vast panel for variants present in conserved ancestral genes, they could identify which genetic variants had been retained by both species through their historical evolution, and which had been actively selected during domestication and improvement. The analysis effectively separates the noise of random genetic drift from the signal of convergent adaptation, spotlighting the variants that two independent crop lineages converged upon under shared environmental pressures.

In wheat, the team validated the role of three genes already characterized in other species, confirming that their ancestral context translates into real function in this staple crop. Two of these genes affect yield and flowering date respectively—traits that breeders manipulate constantly—while the third is implicated in epigenetic regulation, potentially modulating how genes are switched on and off. The validation demonstrates that the paleogenomic workflow is not merely a descriptive exercise: it delivers concrete, testable gene targets whose functions carry over across species boundaries. It also suggests that regulatory genes, not just structural ones, may have been under selection as crops adapted to their environments.

Recognizing that such a resource is most valuable when it is widely accessible, the researchers developed two free, open-access computational tools. The first, named AGR (Ancestral Genome Reconstruction), allows users to compare the genomes of modern plants and reconstruct the vanished founder paleogenomes, producing an expert-validated repertoire of genes conserved between species. The second, OrthoViewer, is a database providing access to these conserved genes across all 84 species of agronomic interest in the study. It integrates 1,142 genes described in the scientific literature with documented biological functions and agronomic relevance. Together, the tools let scientists and private breeders compare global genetic diversity data across species and pinpoint adaptive genetic variants that have been selected jointly in multiple crops—a shortlist of candidates for the next generation of breeding programs.

The implications for climate change adaptation are direct. As temperatures rise and rainfall patterns become less predictable, breeders urgently need sources of tolerance to heat, drought, and new disease pressures. The conserved adaptive variants identified in wheat and barley offer a genetically grounded starting point: variants already proven by evolutionary history to function under stressful conditions. Rather than waiting decades for random recombination to surface useful traits, breeders can deliberately introduce or select these variants in their crossing programs, accelerating the development of varieties suited to the agro-ecological conditions of the future.

Crucially, the method is not confined to cereals. Because it rests on founder paleogenomes built from 84 species spanning many botanical families, including crops currently in cultivation, the workflow can in principle be applied to any plant of agronomic interest. The teams are already extending the approach, hunting for retained adaptive variants in rice, maize, and sorghum as well as in wheat and barley. As Jérome Salse, Research Director at INRAE, summarized the vision: understanding how genetic variants evolved during the domestication and selection of agricultural species allows researchers to identify those selected across species under the same climate constraints—variants of interest for selecting genotypes adapted to the current challenges of climate change and the agro-ecological transition. In short, the answers to tomorrow’s breeding problems may already be written in the deep evolutionary memory of crop genomes, waiting to be read.

Subject of Research: Reconstruction of ancestral plant genomes to identify conserved genes for climate-adaptive crop breeding in wheat and barley.

Article Title: Varietal selection in response to climate change: possible solutions could lie in the history of wheat and barley genes

Article References: Varietal selection in response to climate change: possible solutions could lie in the history of wheat and barley genes. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: paleogenomics, wheat, barley, climate change adaptation, crop breeding, ancestral genome reconstruction, genetic variants, domestication, AGR tool, OrthoViewer, drought tolerance, agronomy

The method, detailed in the prestigious journal Nature Genetics, revolutionizes the way we perceive non-coding regions of the genome. Unlike traditional genetics, which focuses on genes coding for proteins, this approach elucidates the functional significance of regulatory elements—commonly referred to as transcription factor binding sites—that modulate the timing, location, and levels of gene activity. Essentially, these switches operate like dimmer controls for gene expression, finely tuning plant development and stress responses.

Natural genetic variation, indispensable for evolutionary adaptation, underlies the biodiversity observed within plant species. However, the timescale of evolution spans millennia, starkly at odds with the rapid pace of current climate change, manifesting in prolonged periods of drought and other environmental stresses. Understanding and harnessing the subtle genetic variations that govern plant responses is crucial for accelerating the breeding of crops equipped to thrive under these increasingly harsh conditions, thereby safeguarding global food security.

The international collaboration, spearheaded by Dr. Thomas Hartwig and Dr. Julia Engelhorn, focused on analyzing twenty-five distinct maize hybrids, representative crosses between diverse maize varieties. Through their novel method, they pinpointed over 200,000 genomic loci where natural variations influence regulatory switches. This represents an unprecedented scale of resolution in mapping the plant’s genomic “control panel,” opening up vast new territories for functional genomics exploration.

Dr. Engelhorn emphasized that although these regulatory switches occupy less than one percent of the maize genome, they often explain a surprisingly large portion of heritable trait variation, sometimes exceeding fifty percent of the phenotypic differences passed from parent to offspring. This insight challenges the gene-centric paradigm of trait inheritance and underscores the regulatory genome’s pivotal role.

Crucially, the technique allows for a sophisticated comparison of allelic variants inherited from both maternal and paternal lines within a single experimental framework. This capacity to discern lineage-specific regulatory differences provides invaluable data for breeding strategies, enabling researchers to trace how divergent regulatory sequences contribute distinctly to phenotype.

Beyond mapping these switches, the team applied their methodology to traits related to drought stress, identifying more than 3,500 regulatory sites linked to genes involved in water deficit responses. These sites are potential targets for precise modulation, through breeding or biotechnological interventions, to enhance maize’s resilience to water scarcity—a challenge that looms large amid global climate volatility.

Dr. Hartwig highlighted the transformative potential of deciphering the functional mechanics of these regulatory switches. By understanding how variations alter transcription factor binding and downstream gene expression, scientists can pinpoint actionable targets for manipulating traits with a level of specificity and predictability unattainable by previous genetic approaches.

The methodology’s power stems in part from its capacity to connect sequence variants within regulatory regions to tangible changes in transcription factor affinity. Illustrated metaphorically by the team, transcription factors resemble tractors binding to genetic “switches” that toggle gene activity. Variations in the switch sequences can strengthen or weaken this binding, ultimately shifting plant traits such as size, stress tolerance, or growth rate.

This research also confronts the longstanding enigma of the “dark matter” of the genome—the vast non-coding regions once dismissed as “junk DNA.” Through innovative experimental design and integrative genomics, the authors illuminate these previously opaque regions, revealing their critical regulatory functions and transforming our understanding of heritability and trait modulation.

Collaborating closely with researchers from the University of California, Davis, including Dr. Samantha Snodgrass, the team underscores how this shift from gene-focused to regulation-focused genetics necessitates a paradigm change in biology and crop science. The ability to pinpoint functional elements in the non-coding genome equips breeders and molecular biologists with refined tools to accelerate crop improvement in the face of urgent environmental challenges.

The success of this study resides within the broader framework of the CEPLAS Cluster of Excellence on Plant Sciences at HHU and MPIPZ, and benefits from support by the European Horizon Europe project BOOSTER. This funding backbone is essential for pushing forward advanced research aimed at developing climate-resilient cereal crops, with maize serving as a vital global staple.

Looking forward, the implications of this method extend beyond maize, offering a blueprint for investigating regulatory variation across agriculturally important species. By precisely deciphering how transcription factor binding sites dictate phenotypes, the path is paved for next-generation breeding technologies that marry genomic insight with practical crop improvement strategies, potentially revolutionizing global agriculture.

This study sets a new benchmark for the integration of genomics, molecular biology, and plant breeding. The confluence of high-resolution mapping of regulatory elements and functional interpretation heralds an era where natural genetic variation inside genomic switches, rather than canonical gene sequences alone, guides the design of crops tailored to withstand evolving climatic pressures.

In summary, by pulling back the curtain on the regulatory genome and illuminating the importance of transcription factor binding variability, this research provides an unprecedented molecular lens on maize’s complex phenotype. Its contributions mark a decisive step toward smarter, more targeted crop breeding, promising robust yields in the face of climatic adversity and reinforcing the foundation of global food security.

Subject of Research: Genetic variation at transcription factor binding sites and their role in phenotypic heritability in maize.

Article Title: Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize

News Publication Date: 11-Aug-2025

Web References:
http://dx.doi.org/10.1038/s41588-025-02246-7

References:
Engelhorn, J., Snodgrass, S.J., Kok, A., Seetharam, A.S., Schneider, M., Kiwit, T., Singh, A., Banf, M., Khaipho-Burch, M., Runcie, D.E., Camargo, V.S., Torres-Rodriguez, J.V., Sun, G., Stam, M., Fiorani, F., Schnable, J.C., Bass, H.W., Hufford, M.B., Stich, B., Frommer, W.B., Ross-Ibarra, J., Hartwig, T. (2025). Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize. Nature Genetics.

Image Credits: HHU/Andi Kur (licensed under BY-NC-SA)

Keywords: Plant sciences, Signal transduction, Genomic regulatory switches, Transcription factor binding sites, Phenotypic heritability, Maize, Drought stress, Crop resilience, Genetic variation, Plant breeding, Climate change adaptation