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Genotype data of 970 Pedunculate oak trees (Quercus robur L.) in Russia and neighbouring countries at 385 gene loci covering the nuclear and organelle genome

Citation

Degen, Bernd et al. (2022), Genotype data of 970 Pedunculate oak trees (Quercus robur L.) in Russia and neighbouring countries at 385 gene loci covering the nuclear and organelle genome, Dryad, Dataset, https://doi.org/10.5061/dryad.1zcrjdfsc

Abstract

The data set is the result of genetic inventory on 970 Pedunculate oak trees from 97 locations in Russia, Belarus, Ukraine and Latvia representing the eastern part of the natural species range. The data set includes the sample IDs, geographic coordinates of each sampled tree (longitude and latitude in decimal degrees) and the genotype data. All samples were screened with a set of 385 gene markers covering the nuclear (n=364) and the organelle genomes (chloroplast: n=14, mitochondria: n=7) by use of a genotyping by sequencing approach. With exception of three INDELs (Insert and Deletion mutations) all gene markers are SNPs (Single nucleotide Polymorphism).

Methods

At each location ten individual trees were collected. The majority of the samples (85 locations) were collected in natural forest stands and in artificial regenerated stands (7 locations). We set a minimum diameter of 20 cm at breast height and trees separated by a minimum of 50m to reduce the probability to collect related trees. For five locations the material has been collected in a provenance trial which was created in the USSR under the supervision of A. M. Shutyaev on the territory of the Krapivensky forest enterprise-college by employees of the Research Institute of Forest Genetics and Breeding in 1976-1977.

All samples were screened with a set of 385 gene markers covering the nuclear (n=364) and the organelle genomes (chloroplast: n=14, mitochondria: n=7) by use of a genotyping by sequencing approach. With exception of three INDELs (Insert and Deletion mutations) all gene markers are SNPs (Single nucleotide Polymorphism). The details of the used gene markers are given by Degen et al. (2021).

Usage Notes

The genotype of each individual is one row in the table “genotypes” in the EXCEL-file. The genotypes at the nuclear markers are diploid and represented by two columns per gene marker. The genetic information at the organelle genome is haploid. For each of these gene markers one column is used. Genotypes are coded by Arabic numbers. The meaning of the numbers is explained in the table “coding genotypes” in the EXCEL-file.

Funding

German Federal Ministry of Food and Agriculture & German Federal German Ministry for the Environment, Nature Conservation and Nuclear Safety, Award: Waldklimafonds WKF-WF04-22WC4111 01

Russian Science Foundation, Award: grant No 19-16-00084