Selective Breeding is the process of improving one or more desirable traits of a cultured species through the selection of superior parents for the next generation. A breeding program is the implementation of a selective breeding strategy and the set of tools needed to deliver the desired outcomes. The approach selected should be designed to maximize the economic return by balancing input costs and with the expected genetic and economic gains for a commercial aquaculture producer. The use of molecular markers is by far one of the main scientific tools used to help manage breeding programs today.
While there are several genetic marker types available that can be used for this analysis, the single nucleotide polymorphism (SNP) is the most desirable type because SNPs are much more abundant in the animals’ genome than other types of markers. SNPs are also easily assayed and scored in a high-throughput and cost-effective manner. The recent development of industry-wide, single nucleotide polymorphism (SNP) genotyping panels from 200 to 50,000 SNPs provides access to such tools at a very reasonable cost. The choice of how many SNPs to use will be dependent on the objectives of the analysis and the complexity of the breeding populations being investigated; it can be customized for any program, any species, and any budget. These molecular markers can be used in the breeding practice for assessment of diversity parameters, evaluation of consanguinity, pedigree assignment and inference of the structure of the population. However, for more sophisticated applications, such as identification of trait associated markers or genomic selection, larger number of SNPs, > 10,000 must be used. We have developed a powerful 50,000 SNP tool (AquaArrayHD vannamei) designed to work in all shrimp populations to deliver sophisticated results at an industry leading price.
With the development of DNA tools and the understanding of breeding strategies, the economic costs for incorporating genomic selection to accelerate shrimp breeding programs are no longer barriers to implementation. Application of genomic selection is feasible when combining an economically efficient method for scanning the genome of broodstock for SNP (single nucleotide polymorphism) markers and often through the use of genomic imputation to reduce the overall burden of genotyping costs. Genomic selection utilizes either the effects of the genome wide markers or the realized genomic similarity to predict breeding values, rather than pedigree relationships (the expected relatedness). This allows for within family selection resulting in increased selection accuracy such that the breeding candidates with the highest genetic merit from different genetic backgrounds can be identified. Inbreeding can also be controlled in a genome wide fashion. Genomic selection is particularly powerful when selecting for difficult to measure and lowly heritable traits. Among the many benefits of the use of genomic selection for shrimp breeding, is that it would allow for the accurate incorporation of genetic data from ponds without increasing biosecurity risks.