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Genotype data of 1970 Pedunculate oak trees (Quercus robur L.) in 13 European countries at 381 gene loci covering the nuclear and organelle genome

Citation

Degen, Bernd et al. (2021), Genotype data of 1970 Pedunculate oak trees (Quercus robur L.) in 13 European countries at 381 gene loci covering the nuclear and organelle genome, Dryad, Dataset, https://doi.org/10.5061/dryad.8931zcrrd

Abstract

The data set is the result of genetic inventory on 1970 Pedunculate oak trees from 197 locations in Europe. The samples are from the countries: Belarus, Bosnia, Bulgaria, Croatia, Finland, France, Germany, Hungary, Italy, Latvia, Poland, Russia and Ukraine. At each location ten individual trees were collected. The data set includes the location ID and geographic coordinates of each sampled tree (longitude and latitude in decimal degrees) and the genotype data. All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs and five mitochondrial SNPs).

The genotype of each individual is one row in the csv-file “genotypes”. 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 a second csv-file.

Methods

The majority of the samples (188 locations) were collected in forest stands and for nine locations the material has been collected in provenance trials. For the sampling in the forests 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. At each location ten individual trees were collected.

All samples were screened with a targeted sequencing approach on a set of 381 polymorphic loci (356 nuclear SNPs, 3 nuclear InDels, 17 chloroplast SNPs and five mitochondrial SNPs). 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 csv-table “genotypes”. 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 csv-table “coding genotypes”.

Funding

Waldklimafonds, Award: WKF-22WC4111 01

Russian Science Foundation, Award: 19-16-00084