Background: The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot ( Scophthalmus maximus ), gilthead seabream ( Sparus aurata ), European seabass ( Dicentrarchus labrax ) and common carp ( Cyprinus carpio ) to obtain accurate estimates of the effective size for commercial populations. Methods: Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. Results: Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. Conclusions: Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes.

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.

For both undivided and subdivided populations, the consensus method to maintain genetic diversity is the Optimal Contribution (OC) method. For subdivided populations, this method determines the optimal contribution of each candidate to each subpopulation to maximize global genetic diversity (which implicitly optimizes migration between subpopulations) while balancing the relative levels of coancestry between and within subpopulations. Inbreeding can be controlled by increasing the weight given to within‐subpopulation coancestry (λ). Here we extend the original OC method for subdivided populations that used pedigree‐based coancestry matrices, to the use of more accurate genomic matrices. Global levels of genetic diversity, measured as expected heterozygosity and allelic diversity, their distributions within and between subpopulations, and the migration pattern between subpopulations, were evaluated via stochastic simulations. The temporal trajectory of allele frequencies was also investigated. The genomic matrices investigated were (i) the matrix based on deviations of the observed number of alleles shared by two individuals from the expected number under Hardy–Weinberg equilibrium; and (ii) a matrix based on a genomic relationship matrix. The matrix based on deviations led to higher global and within‐subpopulation expected heterozygosities, lower inbreeding and similar allelic diversity than the second genomic and pedigree‐based matrices when a relatively high weight was given to the within‐subpopulation coancestries (λ ≥ 5). Under this scenario, allele frequencies moved only slightly away from the initial frequencies. Therefore, the recommended strategy is to use the former matrix in the OC methodology giving a high weight to the within‐subpopulation coancestry.

The proceedings of the 12th World Congress on Genetics Applied to Livestock Production provide you with 816 papers representing the leading research in livestock genetics around the globe. This boo...