Researchers from INRAE, the University of Clermont Auvergne, and the CNRS have reconstructed 10 ancient genomes, or paleogenomes, that are considered the common ancestors of 84 plant species of agronomic importance. These plants include crops like wheat and barley, which are vital to global food production. The study has identified specific genes shared across different species that may be crucial for adapting to environmental stressors such as drought. By comparing the genes of wheat and barley, the team found around 100 genetic variants that helped these crops survive and thrive as they evolved over 10,000 years of human cultivation and selection. To support future research and breeding efforts, the team developed two open-access tools. These tools, described in the journals Molecular Plant and Nature Plants, offer new possibilities for selecting plant varieties that can better withstand the challenges of climate change. Scientists and plant breeders can now use these resources to identify and study genes that might enhance a plant’s resilience or productivity. The researchers analyzed the genomes of 84 modern flowering plants, which represent a wide range of cultivated species. From this data, they reconstructed 10 ancestral genomes that are more than 200 million years old. These genomes are referred to as "founder" genomes because they represent the genetic blueprint from which modern species evolved. By comparing these ancient genomes with modern ones, the researchers were able to identify genes that have retained their original function and genomic context across different plant species, suggesting they may still be useful in modern agriculture. Wheat and barley were chosen for this study because they are among the oldest domesticated crops and have played a central role in the development of agriculture. Both crops were first cultivated over 10,000 years ago in the Fertile Crescent, a region in the Middle East. Their long history of cultivation and similar environmental challenges make them ideal for studying how genetic traits have been preserved and adapted over time. The researchers examined 1,420 modern varieties of wheat and barley, along with ancient wheat samples from 5,000 years ago, to identify the genetic changes that occurred during their evolution. The study revealed genetic variants that have been key to the survival and productivity of wheat and barley. For example, researchers confirmed the role of three known genes: two that influence yield and flowering time, and a third involved in epigenetic regulation, which can affect how genes are expressed without changing the DNA sequence itself. These findings could help breeders develop crops that are better suited to changing environmental conditions. The two new tools developed by the research team, AGR and OrthoViewer, are designed to help scientists compare and identify genes of interest in cultivated plants. AGR allows researchers to reconstruct ancient genomes and compare them with modern ones, while OrthoViewer provides a database of 1,142 genes known for their biological and agronomic significance. These tools can be applied to a wide range of plant species, and the researchers are now expanding their work to include other major crops such as rice, maize, and sorghum, with a focus on identifying genetic variants that contribute to adaptation and resilience.