DOI: 10.5061/dryad.np8708k2
title: Data from: Scanning SNPs from a large set of expressed genes to assess the impact of artificial selection on the undomesticated genetic diversity of white spruce

description: A scan involving 1134 single-nucleotide polymorphisms (SNPs) from 709
 expressed genes was used to assess the potential impact of artificial
 selection for height growth on the genetic diversity of white spruce. Two
 case populations of different sizes simulating different family selection
 intensities (K = 13% and 5%, respectively) were delineated from the Quebec
 breeding program. Their genetic diversity and allele frequencies were
 compared with those of control populations of the same size and geographic
 origin to assess the effect of increasing the selection intensity. The two
 control populations were also compared to assess the effect of reducing
 the sampling size. On one hand, in all pairwise comparisons, genetic
 diversity parameters were comparable and no alleles were lost in the case
 populations compared with the control ones, except for few rare alleles in
 the large case population. Also, the distribution of allele frequencies
 did not change significantly (P ≤ 0.05) between the populations compared,
 but ten and nine SNPs (0.8%) exhibited significant differences in
 frequency (P ≤ 0.01) between case and control populations of large and
 small sizes, respectively. Results of association tests between breeding
 values for height at 15 years of age and these SNPs supported the
 hypothesis of a potential effect of selection on the genes harboring these
 SNPs. On the other hand, contrary to expectations, there was no evidence
 that selection induced an increase in linkage disequilibrium in genes
 potentially affected by selection. These results indicate that neither the
 reduction in the sampling size nor the increase in selection intensity was
 sufficient to induce a significant change in the genetic diversity of the
 selected populations. Apparently, no loci were under strong selection
 pressure, confirming that the genetic control of height growth in white
 spruce involves many genes with small effects. Hence, selection for height
 growth at the present intensities did not appear to compromise background
 genetic diversity but, as predicted by theory, effects were detected at a
 few gene SNPs harboring intermediate allele frequencies.
description: Large populations
 datasetThe file contains 142
 lines and 1136 columns. In the first column, tree identifyers can be
 found. In the second column, the population type (Case or Control) is
 presented. The 1134 remaining columns contain the genotype of each tree
 for the 1134 SNPs used in this study. More information about these SNPs
 and the genes on which they are located will be provided in Genbank in
 early 2012.Small populations
 datasetThe file contains 56
 lines and 1136 columns. In the first column, tree identifyers can be
 found. In the second column, the population type (Case or Control) is
 presented. The 1134 remaining columns contain the genotype of each tree
 for the 1134 SNPs used in this study. More information about these SNPs
 and the genes on which they are located will be provided in Genbank in
 early 2012.