Pangenome analysis of beech

Lead Institute FG Institute of Forest Genetics

Aerial view of an experimental site from a 30-year-old beech provenance trial

In the project 'PanB' we want to elucidate the role of structural genetic variation in adaptive differentiation of European beech and study the effects of genotype-environment interactions in two parallel common gardens.

Background and Objective

European beech (Fagus sylvatica L.) is a foundation 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 adaptive 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.

Approach

We first want to generate a beech pangenome. This pangenome will capture genome-wide structural genetic variation, i.e., large-scale DNA sequence polymorphisms, across the distribution range. To this end, we will generate long-read PacBio HiFi sequencing data and haplotype-resolved genome assemblies of 72 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 more than 1,000 and 2,000 trees from the common gardens in France and Germany, respectively, onto the pangenome graph and inferring structural variants, we will be able to perform pan-genome-wide association studies (panGWAS) and pangenomic genotype-environment association (panGEAs) analyses. Further, we will analyze the effects of sequence variants underlying phenotypic variation under the two naturally contrasting environments to understand the extent of genotype-environment interactions. These interactions could be essential for genomic predictions 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 adaptive differentiation and support the prediction of future ecosystem stability.

Thünen-Contact

Dr. Niels A. Müller

Telephone

+49 4102 696 107

niels.mueller@thuenen.de

FG Institute of Forest Genetics

Involved Thünen-Partners

Lazic, Desanka FG Institute of Forest Genetics

Involved external Thünen-Partners

Institut national de recherche pour l’agriculture, l’alimentation et l’environnement (INRAE)
(Paris, Toulouse, Montpellier, Avignon, Ivry-sur-Seine, Clermont-Ferrand, Rennes, Thiverval-Grignon, Dijon, Orleans, Bordeaux, Pierroton, Frankreich)