Aquaculture America 2021

August 11 - 14, 2021

San Antonio, Texas

GENETIC OVERVIEW TO REVEAL HOW THE CAPTIVE POPULATION WAS, IS, AND SHOULD BE MANAGED

Adriana Artiles*, E Hu, Anu Frank-Lawale, Melissa Allen, Richard Towner, Salvador Gezan, John Buchanan
 The Center for Aquaculture Technologies.
8395 Camino Santa Fe . Suite E.
San Diego, CA, 92121
aartiles@aquatechcenter.com

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 p roprietary  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 H igh 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 (o bserved 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, t he 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 h istory 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.