Large-Scale Genomic SNP Dataset for Central and Southeast European Turkey Oak (Quercus cerris L.) Populations Generated by ddRAD-Seq Method

Abstract

Background: In Central and Southeast Europe, oak-dominated forests form the backbone of temperate forest ecosystems. Therefore, their adaptability is crucial for maintaining the biodiversity of these ecosystems under ongoing climate change. Turkey oak (Quercus cerris L.) is a widespread species in these regions and holds significant potential for local forestry adaptation due to its drought-tolerant characteristics. Aims: In this study, we investigated natural-origin populations of the species across the Carpathian Basin and the Balkan Peninsula. Our objective was to construct a genomic dataset of single nucleotide polymorphisms (SNPs) to facilitate detailed analyses of the biogeography, genetic diversity, population structure, local selection and adaptation of Turkey oak. Materials & Methods: A total of 32 populations were sampled within the study regions, mostly covering the habitat range of the species in those areas. To obtain high-resolution genomic information, we applied double digest restriction-site associated DNA sequencing (ddRAD-seq) to genotype 321 individuals. We performed SNP calling using reference mapping on the Turkey oak and cork oak genomes. In addition to genetic data, tree-ring and soil data were also collected to enable genotype-phenotype and genotype-environment associations. Results: As a result, two datasets were generated, containing 229,026 and 201,829 genome-wide SNP loci mapped to the Turkey oak and cork oak genomes, respectively. The genotype data were also supplemented with scanned images of tree-ring samples and soil data, which are provided as metadata within the same repository. Discussion: The scale and design of the sampling scheme provide significant opportunities to explore the genetic diversity, population structure, gene flow and biogeography of Turkey oak in Central and Southeast Europe. In addition, supplementary tree-ring and soil data enable conducting various genotype-phenotype/environment associations. Conclusion: The SNP data, along with additional tree-ring and soil data, are available with the following link, providing resources for future research on the species' genetics and biogeography: https://doi.org/10.5061/dryad.pk0p2ngzz.