Plants of different species share common genes that could be important in driving adaptation to specific environmental constraints. The teams set out to discover how knowledge of a gene's role in one species could be applied to the study of another species of interest for plant breeding. They analysed and compared 84 genomes from modern flowering plants that are representative of cultivated plants across the world. This allowed them to reconstruct 10 ancestral paleogenomes over 200 million years old that can be described as the 'founder' genes for modern species. These paleogenomes make it possible to identify genes that have conserved a shared genomic ancestral context and the same biological function, meaning that they could still contribute today to traits or processes across different species. Such genes potentially drive the development of traits of interest for modern agricultural challenges, such as drought tolerance or flowering dates. Beyond the identification of genes of major agronomic interest, the reconstruction of paleogenomes also brings key knowledge on the evolutionary history of plants. In particular, it has enabled the team to establish the timing of the emergence of the major botanical families, and has allowed them to retrace key evolutionary trajectories, for example, those leading to divergence between aquatic and terrestrial plants, between herbaceous and woody species, between C3 and C4 species, and between modulator and non-modulator species.
Genes from over 1000 varieties of wheat and barley compared
Wheat and barley were selected as the focus of the study, both being grain crops of major agronomic interest. They figure among the earliest crops to have been domesticated over 10,000 years ago in the Fertile Crescent. These two cereals supported the emergence of agriculture, displaying considerable parallels in both their historical timelines and the environmental conditions under which they have been cultivated by humans, making them highly relevant to the analysis and comparison of key retained genes. The researchers studied and compared 1,420 modern varieties representative of the global genetic diversity of wheat and barley, along with the remains of ancient wheat from 5,000 years ago. This enabled them to identify the genetic variants that had been retained by both species in the course of their historical evolution. In wheat, the team validated the role of three known genes from other species, two of which affect yield and flowering date, respectively, while the third is implicated in epigenetic regulation (potentially modulating gene activation). Comparison of the paleogenomes shared by these species provided information on both the retained genes and the selected adaptive genes in wheat and barley populations that have evolved under similar climate constraints, requiring them to adapt to similar environments in the course of ten millennia of domestication and selection by humankind. The identification of these variants opens up new avenues for varietal selection programmes, particularly in the context of agricultural adaptation to climate change.
Two open access tools to compare and identify genes of interest in cultivated plants
Dans le cadre de ces travaux, deux outils informatiques en accès libre et gratuits, exploitables par la communauté scientifique et les sélectionneurs privés, ont été développés. Le premier, nommé AGR ( Ancestral genome reconstruction ), permet la comparaison de génomes de plantes modernes et la reconstruction de paléogénomes fondateurs disparus délivrant un répertoire expertisé de gènes conservés entre espèces. Le second, OrthoViewer , est une base de données d'accès à ces gènes conservés pour 84 espèces de plantes d'intérêt agronomique, intégrant 1 142 gènes décrits dans la littérature scientifique pour leur fonction biologique et leur intérêt agronomique. Ce catalogue de gènes conservés permet de comparer, entre espèces, les données de diversité génétique disponibles à l'échelle mondiale et d'identifier des variants génétiques adaptatifs sélectionnés conjointement chez différentes espèces et ayant un potentiel intérêt pour la sélection variétale.
UA method that can be applied to multiple species of agronomic interest
The workflow described in this study on wheat and barley can be applied to all plant types, being based on the founding paleogenomes of 84 plant species from many botanical families, including crop species currently in cultivation. The teams are continuing their work on these paleogenomes, seeking to identify genes of interest, with a particular focus on genetic variants with retained adaptive functions in wheat, barley, rice, maize and sorghum.
"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, and that are of interest for the selection of genotypes adapted to the current challenges of climate change and of the agro-ecological transition."
Jérome Salse, Research Director at INRAE
