Scientists trace 200-million-year-old genomes to breed climate-resilient crops

Researchers have reconstructed ancestral plant genomes more than 200 million years old and used them to pinpoint around 100 gene variants that helped wheat and barley adapt to shifting climates across 10,000 years of human cultivation — variants they say could accelerate the breeding of crops built to withstand hotter, drier growing conditions.

Paleogenomics Meets Modern Breeding

The study, led by teams at INRAE, the University of Clermont Auvergne, and France's CNRS, was published in two papers in Molecular Plant and Nature Plants. By computationally comparing 84 modern flowering-plant genomes, the researchers reconstructed ten "founder" paleogenomes representing the common ancestors of today's crop species. They then scanned 1,420 modern wheat and barley varieties, along with ancient wheat remains dating back 5,000 years, to identify gene variants that both cereals independently retained under similar environmental pressures.bioengineer+3

The logic is straightforward: wheat and barley were domesticated in the same region — the Fertile Crescent — on roughly the same timeline, under the same climatic constraints. When two independently bred species converge on the same genetic variants, those variants are strong candidates for driving real adaptation to drought, heat, and irregular rainfall.phys

Validated Targets and Open Tools

In wheat, the team validated three genes previously characterized in other species. Two affect yield and flowering date, traits breeders already manipulate, while the third plays a role in epigenetic regulation — how genes are switched on or off. The confirmation that these genes function across species boundaries is central to the study's promise: rather than studying each crop in isolation, breeders can use the conserved gene catalog as a translational bridge.newsminimalist+1

To make those results broadly accessible, the researchers released two open-access tools. AGR (Ancestral Genome Reconstruction) lets users reconstruct extinct paleogenomes from modern genome comparisons, while OrthoViewer provides a database of conserved genes across all 84 species studied, integrating 1,142 genes with documented agronomic functions.phys+1

From Cereals to a Broader Toolkit

The method is not limited to wheat and barley. Because the paleogenomes span dozens of botanical families, the workflow can be extended to other staple crops. The teams are already applying it to rice, maize, and sorghum.phys+1

"Understanding how genetic variants have evolved in the course of the domestication and selection of plant and animal species of agricultural interest enables us to identify those that have been selected across species in environments with the same climate constraints," said Jérôme Salse, research director at INRAE. Those variants, he said, are "of interest for the selection of genotypes adapted to the current challenges of climate change and the agroecological transition."phys