Pangenome analysis of European beech to elucidate the role of structural genetic variation in local adaptation and phenotypic differentiation under different environments

• Applicant: Dr. Niels Müller
• Subject Area: Forestry ; Plant Genetics and Genomics
• Term: since 2024
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 545520056

European beech (Fagus sylvatica L.) is a keystone forest tree species in Europe with major ecological, economic, and cultural roles. While it is predicted to be negatively affected by climate change, its large ecological amplitude and high levels of genetic diversity may provide substantial adaptive potential. In the proposed project, we want to elucidate the role of structural genetic variation in adaptative differentiation and study the effects of genotype-environment interactions in two parallel common gardens in France and Germany, to support predictions about future performance of beech forest ecosystems. To this end, we first want to generate a beech pangenome. This pangenome will capture genome-wide structural genetic variation, that is large-scale DNA sequence polymorphisms such as insertions or deletions, across the distribution range. For this, we will select, sequence and assemble 24 genetically diverse beech individuals originating from different geographic regions and expressing different phenotypes. Additionally, we will perform drone-based high-throughput phenotyping of adaptive traits, such as leaf phenology, in the two common gardens, which comprise trees from 102 range-wide populations. By mapping resequencing data from 1,000 and 1,800 trees from France and Germany, respectively, onto the pangenome, we will be able to perform pan-genome-wide association studies (panGWAS) and pangenomic genotype-environment associations (panGEAs). We will analyze the effects of the identified sequence variants underlying phenotypic variation under the two naturally contrasting environments. Understanding the extent of these genotype-environment interactions is essential for genomic predictions of tree performance under current and future conditions. Finally, we want to analyze possible site-specific effects of natural selection in a single generation. In conclusion, the proposed project will provide further insights into the genetic basis of adaptative differentiation and future ecosystem stability.

• DFG Programme: Research Grants
• International Connection: France
• Partner Organisation: Agence Nationale de la Recherche / The French National Research Agency
• Cooperation Partner: Dr. Ivan Scotti