As for most other temperate broadleaved tree species, large-scale genetic inventories of pedunculate oak (Quercus robur L.) have focused on the plastidial genome, which showed the impact of post-glacial recolonization and manmade seed transfer. However, how have pollen mediated gene flow and introgression impacted the large-scale genetic structure? To answer these questions, we did a genetic inventory on 1970 pedunculate oak trees from 197 locations in 13 European countries. All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs, and 5 mitochondrial SNPs). In a former analysis with additional 1763 putative Quercus petraea trees screened for the same gene markers we obtained estimates on the species admixture of all pedunculate oak trees. We identified 13 plastidial haplotypes, which showed a strong spatial pattern with a highly significant autocorrelation up to a range of 1250 km. Significant spatial genetic structure up to 1250 km was also observed at the nuclear loci. However, the differentiation at the nuclear gene markers was much lower compared to the organelle gene markers. The matrix of genetic distances among locations was partially correlated between nuclear and organelle genomes. Bayesian clustering analysis revealed the best fit to the data for a sub-division into two gene pools. One gene pool is dominating the west and the other is the most abundant in the east. The western gene pool was significantly influenced by introgression from Quercus petraea in the past. In Germany, we identified a contact zone of pedunculate oaks with different introgression intensity, likely resulting from different historical levels of introgression in glacial refugia or during postglacial recolonization. The main directions of postglacial recolonization were south to north and south to northwest in West and Central Europe, and for the eastern haplotypes also east to west in Central Europe. By contrast, the pollen mediated gene flow and introgression from Q. petraea modified the large-scale structure at the nuclear gene markers with significant west–east direction.

We used Double Digest Restriction site associated DNA sequencing (ddRAD) and Miseq to develop new geographically informative nuclear and plastid SNP and indel loci in Quercus robur and Q. petraea. Genotypes derived from sequence data of 95 individuals and two pools of 20 individuals each of Q. robur and Q. mongolica covering the distribution range of the species, were analysed to select geographically informative and polymorphic loci within Germany and Russia. We successfully screened a selected set of 431 nuclear single nucleotide polymorphism (nSNP), six nuclear Indel, six mitochondrial single nucleotide polymorphism (mtSNP) and ten chloroplast single nucleotide polymorphism (cpSNP) loci with a SeqSNP genotyping platform on 100 individuals Quercus petraea from 10 locations in Germany, 100 individuals Quercus robur from ten locations in Germany and 100 individuals Quercus robur from ten locations in Russia. The newly developed loci are useful for species identification and genetic studies on the genetic diversity and genetic differentiation of Quercus robur and Quercus petraea in Europe.

Pedunculate oak (Quercus robur L.) is widely distributed across Europe and serves critical ecological, economic, and recreational functions. Investigating its responses to stressors such as drought, extreme temperatures, pests, and pathogens provides valuable insights into its capacity to adapt to climate change. Genetic and dendrochronological studies offer complementary perspectives on this adaptability. Tree-ring analysis (dendrochronology) reveals how Q. robur has historically responded to environmental stressors, linking growth patterns to specific conditions such as drought or temperature extremes. By examining tree-ring width, density, and dynamics, researchers can identify periods of growth suppression or enhancement and predict forest responses to future climatic events. Genetic studies further complement this by uncovering adaptive genetic diversity and inheritance patterns. Identifying genetic markers associated with stress tolerance enables forest managers to prioritize the conservation of populations with higher adaptive potential. These insights can guide reforestation efforts and support the development of climate-resilient oak populations. By integrating genetic and dendrochronological data, researchers gain a holistic understanding of Q. robur’s mechanisms of resilience. This knowledge is vital for adaptive forest management and sustainable planning in the face of environmental challenges, ultimately helping to ensure the long-term viability of oak populations and their ecosystems. The topics covered in this review are very broad. We tried to include the most relevant, important, and significant studies, but focused mainly on the relatively recent Eastern European studies because they include the most of the species’ area. However, although more than 270 published works have been cited in this review, we have, of course, missed some published studies. We apologize in advance to authors of those relevant works that have not been cited.

The genetic composition of 5797 white oaks assigned in forest inventories as Quercus robur (3342), Quercus petraea (2090), Quercus pubescens (170), or as unspecified Quercus. spp. (195) sampled all over Europe were genotyped at 355 nuclear SNPs and 28 maternally inherited SNPs of the chloroplast and mitochondria. The sampling had a focus on Central and Eastern Europe, as well as the Black Sea and Caucasus region. Using a sparse nonnegative matrix factorization (snmf) algorithm, the nuclear genetic information was best represented by K = 4 different genetic clusters, whereas a principal component analysis visualized three different groups. The snmf run with K = 3 corresponded, for most individuals with the assignment in the forest inventories, to the three different species. The majority of the samples (88%) had an admixture coefficient q > 0.8 for one of the three species clusters, underlining the species integrity with a minor level of admixture. In contrast to Q. petraea, Q. robur and Q. pubescens showed a clear geographic genetic substructure. These large-scale within-species genetic structures were correlated to regionally variable levels of introgression between the species. For Q. petraea, introgression from Q. robur and Q. pubescens was less focused to particular regions, and this widespread inter-specific gene flow reduced the geographic genetic differentiation. The genetic variation at the maternally inherited SNPs led to 12 different haplotypes with a clear cross-species geographic pattern, further supporting the observation of significant hybridization and introgression among the species.

The gene pool of populations of pedunculate oak (Quercus robur L.) from the north of the Russian part of the range of the species was studied using a set of 94 SNP loci. They were developed using the new generation DNA sequencing technology (ddRAD). Similar levels of genetic diversity were found in isolated stands with a small number of trees (expected heterozygosity H_E = 0.313 ± 0.011, observed heterozygosity H_O = 0.334 ± 0.004, allelic diversity υ_a = 1.540 ± 0.021, coefficient of inbreeding F_IS = –0.067) and in relatively large populations (H_E = 0.306 ± 0.010, H_O = 0.318 ± 0.012, υ_a = 1.530 ± 0.021, F_IS = –0.039). Statistically significant levels of interpopulation differentiation and population fixation (delta_T = 0.0993; Gregorius genetic distances d₀ = 0.104–0.144, F_ST = 0.0725) were detected. Bayesian cluster analysis allowed identifying genetically distinct genetic groups. The results obtained are discussed taking into account the history of the distribution of pedunculate oak in the north of its range.

To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of Asian Q. mongolica as a reference, we identified 861 variant sites (672 single nucleotide polymorphisms (SNPs); 189 insertion/deletion (indel) polymorphism) from representative species of three continents (Q. mongolica from Asia; Q. petraea and Q. robur from Europe; Q. alba from North America), and we identified additional chloroplast polymorphisms in pools of 20 individuals each from Q. mongolica (789 variant sites) and Q. robur (346 variant sites). Genome sequences were screened for insertion/deletion (indel) polymorphisms to develop markers that identify continental origin of oak species, and that can be easily evaluated using a variety of detection methods. We identified five indel and one SNP that reliably identify continent-of-origin, based on evaluations of up to 1078 individuals representing 13 white oak species and three continents. Due to the size of length polymorphisms revealed, this marker set can be visualized using capillary electrophoresis or high resolution gel (acrylamide or agarose) electrophoresis. With these markers, we provide the wood trading market with an instrument to comply with the U.S. and European laws that require timber companies to avoid the trade of illegally harvested timber.