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Abstract Key message Mining genome-wide DNA sequences enabled the discovery of near-diagnostic markers for species assignment in four European white oaks (Quercus petraea (Matt.) Liebl., Quercus pubescens Willd., Quercus pyrenaica Willd., and Quercus robur L.) despite their low interspecific differentiation. Near-diagnostic markers are almost fully fixed in one species and absent in the three others. As a result, only a handful of markers are needed for species identification, making this genetic assay a very promising operational taxonomic assignment procedure in research and forestry. Context Identifying species in the European white oak complex has been a long-standing concern in taxonomy, evolution, forest research, and management. Quercus petraea (Matt.) Liebl., Q. robur L., Q. pubescens Willd., and Q. pyrenaica Willd. are part of this species complex in western temperate Europe and hybridize in mixed stands, challenging species identification. Aims Our aim was to identify near-diagnostic single-nucleotide polymorphisms (SNPs) for each of the four species that are suitable for routine use and rapid diagnosis in research and applied forestry. Methods We first scanned existing whole-genome and target-capture data sets in a reduced number of samples (training set) to identify candidate diagnostic SNPs, i.e., genomic positions being characterized by a reference allele in one species and by the alternative allele in all other species. Allele frequencies of the candidates SNPs were then explored in a larger, range-wide sample of populations in each species (validation step). Results We found a subset of 38 SNPs (10 for Q. petraea, 7 for Q. pubescens, 9 for Q. pyrenaica, and 12 for Q. robur) that showed near-diagnostic features across their species distribution ranges with Q. pyrenaica and Q. pubescens exhibiting the highest (0.876) and lowest (0.747) diagnosticity, respectively. Conclusions We provide a new, efficient, and reliable molecular tool for the identification of the species Q. petraea, Q. robur, Q. pubescens, and Q. pyrenaica, which can be used as a routine tool in forest research and management. This study highlights the resolution offered by whole-genome sequencing data to design near-diagnostic marker sets for taxonomic assignment, even for species complexes with relatively low differentiation.

Abstract Background Global warming raises serious concerns about the persistence of species and populations locally adapted to their environment, simply because of the shift it produces in their adaptive landscape. For instance, the phenological cycle of tree species may be strongly affected by higher winter temperatures and late frost in spring. Given the variety of ecosystem services they provide, the question of forest tree adaptation has received increasing attention in the scientific community and catalyzed research efforts in ecology, evolutionary biology and functional genomics to study their adaptive capacity to respond to such perturbations. Results In the present study, we used an elevation gradient in the Pyrenees Mountains to explore the gene expression network underlying dormancy regulation in natural populations of sessile oak stands sampled along an elevation cline and potentially adapted to different climatic conditions mainly driven by temperature. By performing analyses of gene expression in terminal buds we identified genes displaying significant dormancy, elevation or dormancy-by-elevation interaction effects. Our Results highlighted that low- and high-altitude populations have evolved different molecular strategies for minimizing late frost damage and maximizing the growth period, thereby increasing potentially their respective fitness in these contrasting environmental conditions. More particularly, population from high elevation overexpressed genes involved in the inhibition of cell elongation and delaying flowering time while genes involved in cell division and flowering, enabling buds to flush earlier were identified in population from low elevation. Conclusion Our study made it possible to identify key dormancy-by-elevation responsive genes revealing that the stands analyzed in this study have evolved distinct molecular strategies to adapt their bud phenology in response to temperature.