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In many ways dogs are an ideal model for the study of genetic erosion and
population recovery, problems of major concern in the field of
conservation genetics. Genetic diversity in many dog breeds has been
declining systematically since the beginning of the 1800’s, when modern
breeding practices came into fashion. As such, inbreeding in domestic dog
breeds is substantial and widespread and has led to an increase in
recessive deleterious mutations of high effect as well as general
inbreeding depression. Pedigrees can in theory be used to guide breeding
decisions, though are often incomplete and do not reflect the full history
of inbreeding. Small microsatellite panels are also used in some cases to
choose mating pairs to produce litters with low levels of inbreeding.
However, the long-term impact of such practices have not been thoroughly
evaluated. Here, we use forward simulation on a model of the dog genome to
examine the impact of using limited markers panels to guide pairwise
mating decisions on genome-wide population level genetic diversity. Our
results suggest that in unmanaged populations, where breeding decisions
are made at the pairwise- rather than population-level, such panels can
lead to accelerated loss of genetic diversity at genome regions unlinked
to panel markers, compared to random mating. These results demonstrate the
importance of genome-wide genetic panels for managing and conserving
genetic diversity in dogs and other companion animals.
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