Skip to main content
Dryad

Large‐scale genomic SNP dataset for central and southeast European Turkey oak (Quercus cerris L.) populations generated by ddRAD‐seq method

Lados, Botond Boldizsár12; Molnár, Csilla Éva12; Farkas, Máté12; Benke, Attila12; Bereczki, Katalin12; Nagy, László12; Köbölkuti, Zoltán A.12; Stojnić, Srđan3; Kesić, Lazar3; Karaklić, Velisav3; Ivanković, Mladen4; Postolache, Dragos56; Hartel, Tibor7; Zhelev, Petar8; Mataruga, Milan9; Tomov, Vladimir8; Cseke, Klára1

Research facility: University of Sopron, Forest Research Institute
Published Jul 30, 2025 on Dryad. https://doi.org/10.5061/dryad.pk0p2ngzz

Data files

Jul 30, 2025 version files 1.76 GB

Abstract

In Central and Southeast Europe, oak-dominated forests constitute the backbone of temperate forest ecosystems. Therefore, their adaptability is crucial for maintaining these ecosystems’ biodiversity under the current climate change. In this study, we investigated Turkey oak (Quercus cerris L.) populations in the Carpathian Basin and the Balkan Peninsula, as it is one of the most abundant species in these regions. The goal of our study was to build a genomic SNP dataset to enable detailed analyses of the species' biogeography, genetic diversity, population structure, and local selection and adaptation. To this end, 32 natural populations were sampled in the study regions covering most of the natural habitat range of the species. To obtain large amounts and highly variable genomic information for the sampled populations we applied double digest restriction site-associated DNA sequencing for the genotyping of the 321 sampled individuals. SNP calling was performed by using reference mapping, in which the Turkey oak and the cork oak 2.0 genomes were used as references. With this approach, two datasets were generated allowing future users to obtain information on the markers’ genomic positions which is required e.g. for functional genomic analyses. The dataset mapped to the Turkey oak genome comprising 229 026, whereas the second dataset mapped to the cork oak genome 201 829 highly variable genome-wide SNP loci. Thanks to the scale and the sampling design, there are great opportunities to use these datasets to survey the species’ genetic diversity, population structure, gene flow and investigate the biogeography of Turkey oak in the Central and Southeast European region. In addition, tree-ring and soil data were also included, which can be used for more complex analyses, such as genotype-phenotype or genotype-environment associations, as well as dendrochronological studies.