The last decade has seen wide adoption of incorporating genetic tools into breeding programs across all areas of agriculture. Decreasing costs coupled with advances in technology have made these tools, which were once only utilized by large scale commercial producers, accessible to mid-sized and even smaller scale producers. Modern genotyping technology provides the opportunity to address some of the unique challenges faced in aquaculture such as tracking pedigree, inbreeding avoidance, disease resistance, increasing fecundity, and improvement of growth and meat quality characteristics.
By far, the most widely used genetic marker in modern breeding programs are single nucleotide polymorphisms (SNPs). This type of genetic variant is found abundantly in all genomes, making SNP genotyping technologies a versatile genetic tool that can be designed for any species, is adaptable for for various applications and is scalable, targeting anywhere from one to millions of SNPs. Generally, SNP panels fall into 1 of 4 scale categories; low density, LD (~100-500 SNPs), medium density, MD (1000-5000 SNPs), high density, HD (10,000 to 500,000 SNPs) and, more recently, ultra high density, ultraHD (10 million to 100 million SNPs). The required panel size is usually determined by the type of downstream application, with basic tasks like pedigree tracing and genetic diversity monitoring only requiring a few hundred SNPs, to more complex tasks like genomic selection and genome-wide association studies requiring 30,000+ SNPs.
Here, we demonstrate the creation and downstream application of LD, MD, HD and ultraHD genotyping panels for several well-known and lesser-known aquaculture species. The utility of these panels at accomplishing pedigree tracing, genetic diversity monitoring, QTL identification and genomic selection is discussed. We highlight the ability of SNP genotyping panels to be cost-effective tools to manage genetic diversity and guide breeding strategies to achieve both short-term and long-term breeding goals in modern aquaculture.