DOI: 10.5061/dryad.h44j0zpg5
title: Data from: Parentage and relatedness reconstruction in Pinus sylvestris using genotyping by sequencing

description: Estimating kinship is fundamental for studies of evolution, conservation
 and breeding. Genotyping-by-sequencing (GBS) and other restriction based
 genotyping methods have become widely applied in these applications in
 non-model organisms. However, sequencing errors, depth and reproducibility
 between library preps could potentially hinder accurate genetic
 inferences. In this study, we tested different sets of parameters in data
 filtering, different reference populations and eight estimation methods to
 obtain a robust procedure for relatedness estimation in Scots pine (Pinus
 sylvestris L.). We used a seed orchard as our study system, where
 candidate parents are known and pedigree reconstruction can be compared to
 theoretical expectations. We found that relatedness estimates were lower
 than expected for all categories of kinship estimated if the proportion of
 shared SNPs was low. However, estimates reached expected values if loci
 showing an excess of heterozygotes were removed and genotyping error rates
 were considered. The genetic variance-covariance matrix (G-matrix)
 estimation, however, performed poorly in kinship estimation. The reduced
 relatedness estimates are likely due to false heterozygosity calls. We
 analyzed the mating structure in the seed orchard and identified a selfing
 rate of 3% (including crosses between clone mates) and external pollen
 contamination of 33.6%. Little genetic structure was observed in the
 sampled Scots pine natural populations, and the degree of inbreeding in
 the orchard seed crop is comparable to natural stands. We illustrate that
 under our optimized data processing procedure, relatedness and genetic
 composition, including level of pollen contamination within a seed orchard
 crop, can be established consistently by different estimators.
description: Needles from multiple ramets of each of the 28 genotypes in a
 seed orchard (Västerhus, Sweden) were collected to establish their genetic
 identity. Additional samples from 149 tree genotypes were collected in
 genetic archives and seed orchards across Sweden.  Seeds obtained from a
 bulk collection of cones produced by open pollination in 2014 in the
 orchard, an additional orchard for diversity comparison and two unmanaged
 stands were germinated in a greenhouse. Needles from 300 seedlings from
 each orchard and 50 from each unmanaged stand were harvested in early
 2017. We also included haploid material from two Västerhus genotypes
 (eight megagametophytes each), representing selfed material and 29 samples
 from two congeneric species, <i>Pinus tabuliformis </i>and
 <i>Pinus yunnanensis</i>. In total, 922 samples were collected
 and genotyped. DNA was extracted and GBSlibraries were
 made. Libraries were sequenced using Illumina Hiseq2500  and Illumina
 HiseqX. Samples were de-multiplexed using Stacks:
 <i>process_radtags</i> and then mapped to the <i>Pinus
 taeda</i> genome v1.01 with a Burrows-Wheeler Aligner (BWA). Samples
 were then combine for variant calling with SAMtools
 –<i>mpileup.</i>
description: The dataset contains several files:
 Vasthus_001_m06.vcf.gz: VCF-file which has been slightly pre
 filtered to reduce size, see vcf_filter.txt
 Vasterhus.txt: Sample names of samples in the study
 refkeep.txt: Sample names of the samples used as allele frequency
 reference Parental_ID.txt: The registered names for the
 parental trees in the study vcf_filter.txt: Description
 on how to filter the VCF file according to the manuscript
 Rfiles<br> Dataset-2.RData: The data set resulting from
 working through the vcf filtering and rhe R-script files
 Rcode_related.R: R-script for relatedness estimation using the
 R-package 'related' view_relationships.R:
 Utilizing the result from the previous R-script to visualize pairwise
 relatedness and reconstructing some figures from the manuscript