10.5061/DRYAD.NP8708K2
Namroud, Marie-Claire
Université Laval
Bousquet, Jean
Université Laval
Doerksen, Trevor
Université Laval
Beaulieu, Jean
Université Laval
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
Dryad
dataset
2012
Picea glauca
association genomics
Tree breeding
selection intensity
Sample size
conifer
2012-01-03T19:56:03Z
2012-01-03T19:56:03Z
en
https://doi.org/10.1111/j.1752-4571.2012.00242.x
921181 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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.
Canada
Province of Quebec