A lack of genetically improved strains is consistently noted as an impediment to growth of the aquaculture industry. Genomic selection can help address this need by increasing the rate of genetic improvement in breeding programs . However, t he required genotyping is often cost-prohibitive . Genotyping costs are exacerbated by the high number of aquaculture species, which impedes the reduction of costs through a shared genetic panel (e.g., a high-density SNP array). The aquaculture industry needs a genotyping strategy for genomic selection that can be applied at low volumes across a wide range of species.
One previously described solution is to reserve high-density genotyping for key individuals and apply a low-density SNP panel along with pedigree-based imputation to the remaining individuals. We examined the possibility of further lowering the cost of this strategy by targeting microhaplotypes instead of SNPs in the low-density panel, which could allow smaller panels to be used. We simulated Pacific oyster, eastern oyster, and Atlantic salmon breeding programs for three generations and compared imputation and GEBV accuracy using low-density panels targeting SNPs or microhaplotypes. Panels targeting microhaplotypes yielded higher imputation and GEBV accuracy than that of equally sized panels targeting SNPs. In the Pacific and eastern oyster simulations, close to the maximum imputation and GEBV accuracy was reached when the low-density panel contained 150 - 250 microhaplotypes or 350 - 450 SNPs. In the Atlantic salmon simulations, this level of accuracy was reached with low-density panels of 350 - 450 microhaplotypes or 650 - 750 SNPs. Using low-density panels targeting microhaplotypes instead of SNPs can allow programs to genotype fewer loci, thereby reducing the cost of genotyping. This will make genomic selection feasible for a wider range of aquaculture breeding programs.