Strategies for implementing genomic selection in family-based aquaculture breeding schemes: double haploid sib test populations

Six alternative breeding schemes were simulated in which the design of the test population was varied: test sibs inherited maternal (Mat), paternal (Pat) or a mixture of maternal and paternal (MatPat) double haploid genomes or test sibs were obtained by maximum coancestry mating (MaxC), minimum coancestry mating (MinC), or random (RAND) mating. Three thousand test sibs and 3000 candidate sibs were genotyped. The test sibs were recorded for a trait that could not be measured on the candidates and were used to estimate SNP effects. Selection was done by truncation on genome-wide estimated breeding values and 100 individuals were selected as parents each generation, equally divided between both sexes.Results showed a 7 to 19% increase in selection accuracy and a 6 to 22% increase in genetic gain in the MatPat scheme compared to the RAND scheme. These increases were greater with lower heritabilities. Among all other scenarios, i.e. Mat, Pat, MaxC, and MinC, no substantial differences in selection accuracy and genetic gain were observed.In conclusion, a test population designed with a mixture of paternal and maternal double haploids, i.e. the MatPat scheme, increases substantially the accuracy of selection and genetic gain. This will be particularly interesting for traits that cannot be recorded on the selection candidates and require the use of sib tests, such as disease resistance and meat quality.In traditional aquaculture breeding schemes, selection for traits that cannot be measured on the selection candidates (e.g. disease resistance and fillet quality) is based on a performance test of sibs of the candidates, i.e. information on test sibs is used to calculate breeding values for the selection of parents. This is due to the fact that measuring meat quality traits requires killing of the fish and fish that have been challenge-tested for disease resistance cannot be used as breeding stock. However, with a sib test, only 50% of the total genetic variance of the candid