Changes in Allele Frequencies When Different Genomic Coancestry Matrices Are Used for Maintaining Genetic Diversity

A main objective in conservation programs is to maintain genetic variability. This can be achieved using the Optimal Contributions (OC) method that optimizes the contributions of candidates to the next generation by minimizing the global coancestry. However, it has been argued that maintaining allele frequencies is also important. Different genomic coancestry matrices can be used on OC and the choice of the matrix will have an impact not only on the genetic variability maintained, but also on the change in allele frequencies. The objective of this study was to evaluate, through stochastic simulations, the genetic variability maintained and the trajectory of allele frequencies when using two different genomic coancestry matrices in OC to minimize the loss of diversity: (i) the matrix based on deviations of the observed number of alleles shared between two individuals from the expected numbers under Hardy–Weinberg equilibrium (θ(LH)); and (ii) the matrix based on VanRaden’s genomic relationship matrix (θ(VR)). The results indicate that the use of θ(LH) resulted in a higher genetic variability than the use of θ(VR). However, the use of θ(VR) maintained allele frequencies closer to those in the base population than the use of θ(LH).