Genetic Overview (GO) is a compelling service to characterize populations in captivity that are usually managed for commercial purposes. Using a set of software tools and calculations the GO report describes the levels of diversity, consanguinity, and the genetic structure of the sampled population. These proprietary techniques of the Center of Aquaculture Technologies make use of all types of Single Nucleotide Polymorphisms (SNP) arrays: Low Density (LD), Medium Density (MD) and High Density (HD). These arrays are now available for a variety of aquatic species, including shrimp (Litopenaeus vannamei), oysters (Crassostrea gigas and Crassostrea virginica), and fish (salmon; (Salmo salar), Red snapper (Lutjanus peru), cobia (Rachycentron canadum), yellowtail (Seriola rivoliana, Seriola lalandi), halibut (Hippoglossus hippoglossus), sable fish (Anoplopoma fimbria), among others. The option of design and customization of genomic tools for non-traditional aquaculture species is also available.
The present work describes the parameters of GO used to characterize these cultured stocks and its biological meaning. To protect the confidentiality, synthetic (simulated) data is used for this purpose. Four fictitious breeding lines; AA, BB, CC, and DD are compared to show the meaning of diversity parameters such as the percent of polymorphic loci, the heterozygosity (observed and expected) and the Nei’s diversity index. The extent of consanguinity is assessed by pairwise comparisons of the relatedness coefficient (r). Finally, the structure of the breeding lines based on their differentiation or similarity is explained using the interspecific variation coefficient (Fst), the Principal Coordinates Analysis (PCoA) and the Structure plots.
Some of the applications of this type of analysis will be further summarized. It is particularly powerful in monitoring genetic health over time in breeding programs based on mass selection but is broadly applicable to all programs. In general terms, the Genetic Overview is a snapshot of the current state of the population genetic characteristics. It is highly recommended at the beginning of the breeding programs of all types to understand the level of diversity and relatedness, and the history that the DNA reveals about previous management and origin of the lines, this helping to device sound breeding strategies. Adopting GO into the hatchery practice will help to evaluate the impact of selection and assess the genetic quality of the lines, guide the mating decisions to maximize diversity and decrease the rate of inbreeding/relatedness, and consequently provide an evaluation of the genetic management through the production process.