File name: Fagus_sylvatica_provtrial_BU2012_SI_SNPs_sampleFilt.vcf This (ReadMe) file was created on 2026-01-17 by Marija Kravanja -------------------------------------------------------------------------------------------------------------------------- GENERAL INFORMATION -------------------------------------------------------------------------------------------------------------------------- Name of the dataset: Fagus sylvatica BU2012: A curated genetic dataset for trial trees from the international beech provenance trial "Kamenski hrib/Straža (SI) 1996/1998" Authors, ORCID numbers, e-mails and Institutions/affiliations: Marko Bajc1, 0000-0002-8254-4102, marko.bajc@gozdis.si Gregor Božič1, 0000-0002-5595-2979, gregor.bozic@gozdis.si Marija Kravanja1,2, 0009-0002-1478-6457, marija.kravanja@gozdis.si Sara Pinosio3, 0000-0002-1820-3637, sara.pinosio@cnr.it Francesca Bagnoli3, 0000-0001-6909-0006, francesca.bagnoli@cnr.it Marjana Westergren1, 0000-0002-4204-0161, marjana.westergren@gozdis.si 1 Slovenian Forestry Institute, Večna pot 2, 1000 Ljubljana, Slovenia 2 Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia 3 Institute of Biosciences and BioResources (IBBR), National Research Council (CNR), 50019 Sesto Fiorentino (Firenze), Italy ROR organization identifiers: https://ror.org/0232eqz57 https://ror.org/01gtsa866 Date of data collection: from 2023-05-25 to 2025-06-13 Geographical location of data collection: 45.795304°N, 15.043523°E, Straža, Slovenia Acknowledgements: Data collection and preparation was supported by the EU H2020 FORGENIUS project (grant agreement No. 862221) and the Slovenian Research Agency (core research funding No. P4-0107 and Young Researcher grant No. 58170). We thank Natalija Dovč and Gregor Skoberne for field sampling, and Ilaria Spanu, Barbara Štupar and Veronika Končan for their help with DNA extractions. License: CC BY 4.0 DOI 10.20315/Data.0015 -------------------------------------------------------------------------------------------------------------------------- SHARING/ACCESSING INFORMATION -------------------------------------------------------------------------------------------------------------------------- Data licences/restrictions: CC BY 4.0 Was the data obtained from another source? NO/YES -------------------------------------------------------------------------------------------------------------------------- VIEWING DATA AND FILES -------------------------------------------------------------------------------------------------------------------------- Fagus_sylvatica_provtrial_BU2012_SI_SNPs_sampleFilt.vcf Are there multiple versions of the dataset? NO/YES -------------------------------------------------------------------------------------------------------------------------- METHODOLOGICAL INFORMATION -------------------------------------------------------------------------------------------------------------------------- Description of the methods used to collect/obtain the data: Individuals from 36 provenances of European beech were sampled at the provenance trial Kamenski hrib/Straža (SI) in 2023. Leaves were collected from 23 to 28 trees per provenance and stored in silica gel. DNA was extracted from 20 mg of dried leaf material per individual using NucleoSpin® Plant II kit (Macherey-Nagel). To achieve the DNA quality and quantity required for analyses by Single Primer Enrichment Technology (SPET), i.e. at least 500 ng of DNA/sample with a fluorimetric concentration of 20-50 ng/µl and with absorbance ratios of A260/A280 ≥ 1.7 and 1.6 ≤ A260/A230 ≤ 2.2, the manufacturer’s standard protocol was modified by adding 1ng/µl Proteinase K to the CTAB-based lysis buffer, and extending the lysis process to 1 hour. Genomic DNA was quantified using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). Library preparation, SPET sequencing and SNP detection and filtering were performed following the workflow described by Pinosio et al. (submitted): Pinosio, S., Bagnoli, F., Avanzi, C., Castellani, M. B., Frascella, A., McEvoy, S. L., Olsson, S., Spanu, I., Vajana, E., the FORGENIUS Consortium, González-Martínez, S. C., Pyhäjärvi, T., Scotti, I., Vendramin, G. G., Piotti, A. (2025). The FORGENIUS genomic resources: new genotyping tools and genomic data for 23 forest tree species and their Genetic Conservation Units [Preprint]. bioRxiv. https://doi.org/10.1101/2025.08.08.669074 Experimental conditions, data processing methods, software information, standards and calibration data: See Pinosio et al. (submitted). -------------------------------------------------------------------------------------------------------------------------- DATA-SPECIFIC INFORMATION -------------------------------------------------------------------------------------------------------------------------- List of variables: #CHROM (chromosome identifier), POS (1-based genomic position of the variant), ID (variant identifier), REF (reference base at the position), ALT (alternate allele(s)), QUAL (phred-scaled quality score for the variant call), FILTER (filter status of the variant call), INFO (site-level information), FORMAT fields: GT (genotype), AD (allele depth), DP (total read depth).