European beech, Fagus sylvatica L., is one of the most important and widespread deciduous tree species in Central Europe and is widely managed for its hard wood. The complete DNA sequence of the mitochondrial genome of Fagus sylvatica L. was assembled and annotated based on Illumina MiSeq reads and validated using long reads from nanopore MinION sequencing. The genome assembled into a single DNA sequence of 504,715 bp in length containing 58 genes with predicted function, including 35 protein-coding, 20 tRNA and three rRNA genes. Additionally, 23 putative protein-coding genes were predicted supported by RNA-Seq data. Aiming at the development of taxon-specific mitochondrial genetic markers, the tool SNPtax was developed and applied to select genic SNPs potentially specific for different taxa within the Fagales. Further validation of a small SNP set resulted in the development of four CAPS markers specific for Fagus, Fagaceae, or Fagales, respectively, when considering over 100 individuals from a total of 69 species of deciduous trees and conifers from up to 15 families included in the marker validation. The CAPS marker set is suitable to identify the genus Fagus in DNA samples from tree tissues or wood products, including wood composite products.

New first and 1.5 generation seed orchards are to be created in Germany based on recently assembled breeding populations ofAcer pseudoplatanus,Larixsp.,Picea abies,Pinus sylvestris,Pseudotsuga menziesii, andQuercussp. To justify the high expenses in time and cost for orchard establishment and maintenance, planning should make use of consolidated knowledge and experience of both the national and international scientific community. Here, we briefly describe advances in genetic gains achieved through tree breeding, and resume population genetic aspects and design considerations to draw conclusions for clonal composition and spatial design of the new orchards.We conclude that to avoid outbreeding depression separate orchards are required for each breeding zone. The zones are species-specific and defined by ecological and climatic aspects. A minimum of 60-80 clones per orchard is recommended for native tree species with high proportions of natural regeneration in forest practice. This would allow future selective thinning based on estimated breeding values from progeny testing. It would also permit the transfer of seed orchard progenies into a naturally regenerating forest stands without the risk of a genetic bottleneck. Lower clone numbers are appropriate for non-native species and hybrids. It is important to strictly avoid inbreeding depression, achieved by using only one clone per progeny or population, from which the plus trees were selected. Further, the spatial layout should promote random mating by optimizing the neighbourhood of each clone. With all of these considerations taken into account, we expect superior quality traits and at least 10-15 % more volume from the new seed orchards.