*4.1. Plant Material*

The reference *F. sylvatica* specimen for DNA sequencing (FASYL\_29) was selected for sequencing from a set of genotyped beech trees from a former study [54]. It originates from the German population Gransee/Brandenburg, located in the center of the natural distribution range (53◦00- N, 13◦10- O, 70 m a.s.l.) and was sampled in a progeny test. The parental population is an approved seed stand at the age of about 200 years. The selected individual is a good genetic representative of Central Europe with highest similarities to German, Czech, and Austrian beech populations.

For RNA sequencing, buds of three year old seedlings (HE1 and HE2) grown in a nursery were collected in winter. The seedlings originate from a seed lot harvested in a natural *F. sylvatica* population that is located close to Hengstberg in the Fichtel Mountains in Germany (geo-coordinates of the population: 50◦07- 55--; 12◦11- 18--).

For validation of the developed CAPS markers, leaves or buds from 145 trees of 69 different species and various geographic origins were used. A part of this plant material was sampled in the Arboretum of the Thünen Institute of Forest Genetics in Großhansdorf. Additionally, DNA from specimens of *F. sylvatica* was provided by the projects "GenMon" and "Herkunft Europa" (subproject/project conducted at the Thünen Institute of Forest Genetics). The *Quercus* specimens were provided by the previous project "DBU Weisseiche" and by North American, Russian, and Korean institutions. Different Botanical Gardens provided us also with specimens of other species (Table S5). For the sampling strategy, we always tried to obtain material from different regions of the natural distribution areas of the tree species. Thus, e.g., especially for *F. sylvatica*, individuals from all over Europe were used (Table S5). The use of a broad range of species within the orders and families was particularly important to select "golden" markers with high specificity based on validation.
