Removing exogenous information using pedigree data

Abstract

Management of certain populations requires the preservation of its pure genetic background. When, for different reasons, undesired alleles are introduced, the original genetic conformation must be recovered. The present study tested, through computer simulations, the power of recovery (the ability for removing the foreign information) from genealogical data. Simulated scenarios comprised different numbers of exogenous individuals taking part of the founder population and different numbers of unmanaged generations before the removal program started. Strategies were based on variables arising from classical pedigree analyses such as founders' contribution and partial coancestry. The efficiency of the different strategies was measured as the proportion of native genetic information remaining in the population. Consequences on the inbreeding and coancestry levels of the population were also evaluated. Minimisation of the exogenous founders' contributions was the most powerful method, removing the largest amount of genetic information in just one generation. However, as a side effect, it led to the highest values of inbreeding. Scenarios with a large amount of initial exogenous alleles (i.e. high percentage of non native founders), or many generations of mixing became very difficult to recover, pointing out the importance of being careful about introgression events in populations where these are undesired.

Advantages of using molecular coancestry in the removal of introgressed genetic material

“…However, with the pedigree-based method, the maximum level of removal was achieved in just one generation of management [14], thus on this time scale, it is more efficient. With the molecular-based method, an equivalent level of removal to that obtained with the pedigree-based method was achieved only at the second generation of management (not shown), but it continued to increase in subsequent generations.…”

“…In a previous study, we used pedigree data as source of information to remove introgressed genetic material and recover the native genetic background [14]. Different introgression events were simulated with a varying number of exogenous individuals entering the population and different numbers of generations during which exogenous genetic material was admixed.…”

Optimum contribution selection for conserved populations with historic migration

“…Amador et al [24] proposed two other approaches to reduce migrant contributions. Their first approach was to minimize migrant contributions in the offspring population.…”

“…In contrast, all approaches proposed in this paper aim at increasing the probability that alleles originating from native founders are not IBD. Amador et al [24] concluded that even with only a few generations without management, a small amount of introgression can spread into the population and it may be almost impossible to recover. This was not observed in our study.…”

Use of different sources of information for the recovery and genetic management of endangered populations: Example with the extreme case of Iberian pig Dorado strain

“…In that case, strategies should also be aimed to gradually recover the specific genetic composition of that population. For such a task we may use the genealogical information (if we can trace back to the moment exogenous individuals entered the population) or molecular information (if marker data on the genetic constitution of population before the undesired introgression took place are available; Amador et al, 2011). However, these data are rarely available and, therefore, 'purification' must be based on other information.…”