The power to detect artificial selection acting on single loci in recently domesticated species

Summary

Background: An increasing number of aquaculture species are subjected to artificial selection in systematic
breeding programs. Rapid improvements of important commercial traits are reported, but little is known about the
effects of the strong directional selection applied, on gene level variation. Large numbers of genetic markers are
becoming available, making it feasible to detect and estimate these effects. Here a simulation tool was developed
in order to explore the power by which single genetic loci subjected to uni-directional selection in parallel
breeding populations may be detected.
Findings: Two simulation models were pursued: 1) screening for loci displaying higher genetic differentiation than
expected (high-FST outliers), from neutral evolution between a pool of domesticated populations and a pool of
wild populations; 2) screening for loci displaying lower genetic differentiation (low-FST outliers) between
domesticated strains than expected from neutral evolution. The premise for both approaches was that the isolated
domesticated strains are subjected to the same breeding goals. The power to detect outlier loci was calculated
under the following parameter values: number of populations, effective population size per population, number of
generations since onset of selection, initial FST, and the selection coefficient acting on the locus. Among the
parameters investigated, selection coefficient, the number of generation since onset of selection, and number of
populations, had the largest impact on power. The power to detect loci subjected to directional in breeding
programmes was high when applying the between farmed and wild population approach, and low for the
between farmed populations approach.
Conclusions: A simulation tool was developed for estimating the power to detect artificial selection acting directly
on single loci. The simulation tool should be applicable to most species subject to domestication, as long as a
reasonable high accuracy in input parameters such as effective population size, number of generations since the
initiation of selection, and initial differentiation (FST) can be obtained. Identification of genetic loci under artificial
selection would be highly valuable, since such loci could be used to monitor maintenance of genetic variation in
the breeding populations and monitoring possible genetic changes in wild populations from genetic interaction
between escapees and their wild counterpart.

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DOI : doi.org/http://www.biomedcentr...
NVA : hdl.handle.net/11250/5555953