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

Abstract

Background: When introgression of undesired exogenous genetic material occurs in a population intended to remain pure, actions are necessary to recover the original background. It has been shown that genome-wide information can replace pedigree information for different objectives and is a valuable tool in the fields of genetic conservation and breeding. In this simulation study, molecular information provided by 50 000 SNP was used to minimise the molecular coancestry between individuals of an admixed population and the foreign individuals that originally introgressed a native population in order to remove the exogenous DNA.

Results: This management method, which detects the 'purest' individuals to be used as parents for the next generation, allowed recovery of the native genetic background to a great extent in all simulated scenarios. However, it also caused an increase in inbreeding larger than expected because of the lower number of individuals selected as parents and the higher coancestry between them. In scenarios involving several introgression events the method was more efficient than in those involving a single introgression event because part of the genetic information was mixed with the native genetic material for a shorter period.

Conclusions: Genome-wide information can be used to identify the purest individuals via the minimisation of molecular coancestry between individuals of the admixed and exogenous populations. Removal of the undesired genetic material is more efficient with a molecular-based approach than with a pedigree-based approach.

Figure 1

Design of the two scenarios used in this study. Left: Scenario involving one introgression event. Right: Scenario involving several introgression events.

Figure 2

Native genetic representation and ΔF in the simulation with one introgression event. Native genetic representation is the percentage of native genetic material recovered after one or ten generations of management (upper panels); ΔF is average inbreeding coefficient in the first generation and ΔF₁₀ is the increase of inbreeding over ten generations of management (lower panels) in the one introgression event scenarios (maximum number of offspring per individual = 10); (a) with one non-managed generation; (b) with three non-managed generations; (c) with five non-managed generations.

Figure 3

Native genetic representation and ΔF in the simulation with several introgression events. Native genetic representation is the percentage of native genetic background recovered after one or ten generations of management (upper panels); ΔF is average inbreeding coefficient in the first generation and ΔF₁₀ is the increase of inbreeding over ten generations of management (lower panels) in the several introgression scenarios (maximum number of offspring per individual = 10); (a) with two non-managed generation; (b) with three non-managed generations; (c) with four non-managed generations; (d) with five non-managed generations.