Data from: Parentage and relatedness reconstruction in Pinus sylvestris using genotyping by sequencing

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.