World Aquaculture Magazine -December 2021

WWW.WA S .ORG • WORLD AQUACULTURE • DECEMBER 2021 69 us into the age of the genomic signature, an identity that can genetically explain the superior performance in the field and in the laboratory. Labeling a line with genomic signature is not just a fancy way of branding. It is also an entrance point for genetic resources repositories. The National Animal Germplasm Program of USDA-ARS has already adopted genetic evaluation of all germplasm collections so that better management can be made (US Department of Agriculture 2019). Genomic signature is also a step forward in food safety because the genotypes, especially high-density genotypes, are the most accurate method for establishing traceability. Last but not the least, the sustainability of aquaculture depends on sharing quality information and taking cohesive actions (Bush et al. 2019). Having well-defined lines with field, laboratory and genomic information will be the contribution of shrimp genetics companies to sustainable aquaculture. Notes E Hu, Primo Broodstock USA LLC. Dr. E Hu is a newly appointed executive of Primo Broodstock USA LLC. He applies his genetic resources management expertise to the shrimp broodstock of Primo and uses its disease resistant shrimp line to promote industry-wide standards for valuable genetic lines. References Bush, S.R., P. Oosterveer, M. Bottema, M. Meuwissen, Y. de Mey, S. Chamsai, H.H. Lien and M. Chadag. 2019. Inclusive environmental performance through ‘beyond-farm’aquaculture governance. Current Opinion in Environmental Sustainability 41:49-55. Lillehammer, M., R. Bangera, M. Salazar, S. Vela, E.C. Erazo, A. Suarez, J. Cock, M. Rye and N.A. Robinson. 2020. Genomic selection for white spot syndrome virus resistance in whiteleg shrimp boosts survival under an experimental challenge test. Scientific Reports 10(1):1-13. Ministry of Agriculture and Rural Affairs of the People’s Republic of China. (n.d.). Aquaculture new line evaluation. zwfw.Moa.Gov.Cn/ Nyzw/Index.Html?RedirectValue=82589#/Service/Particulars?Id= 9445066201b74219843831e236e2ac95. Robinson, N. A. and M. Lillehammer. 2020. A genetic solution for tackling white spot syndrome virus in shrimp. thefishsite.com/ Articles/a-Genetic-Solution-for-Tackling-White-Spot-Syndrome- Virus-in-Shrimp. US Department of Agriculture. 2019. National Animal Germplasm Program. www.ars.usda.gov/Plains-Area/Fort-Collins-Co/ Center-for-Agricultural-Resources-Research/Paagrpru/Docs/ Animal/2013-Nagp-Intro/. World Wildlife Fund. (n.d.). Farmed Shrimp. www.worldwildlife.org/ Industries/Farmed-Shrimp. observations and basic stocking information (e.g., density) can still provide some level of confidence when comparing field survival rate. During 2013- 2016, the field data indicated 100-300 percent greater survival in the resistant line (Table 1). Disease Challenge Testing Standardized disease challenge is the most accurate method for collecting disease resistance phenotypes. The standardization also enables the comparison horizontally (i.e., versus other shrimp populations) and vertically (i.e., versus historical populations). University of Arizona provided disease challenge on the resistant lines over the years. In these challenge experiments, the density, dosage, water quality were consistent, therefore the survival of the disease challenge represents the specific pathogen resistance capability under controlled environment. Over the years, the resistant line resisted both WSSV and AHPND toxins (Fig. 1). Although year-to-year variation exists, survival rates of the resistant line are significantly greater than those of other commercial lines. Genomic Signature The most distinguishable characteristics come from the most cutting-edge genotyping technology. The resistant line adopted 50k SNP chips designed for whiteleg shrimp for genotyping. The high-density array provides more than 50,000 genotypes of each broodstock in every generation. These genotypes can be presented via the principal component analysis to show their genetic distance to each other, i.e., similar lines of shrimp will group together. All resistant line generations overlap and form a genetic cluster (Fig. 2). This is an indication of the consistency of the resistant line. Furthermore, the genetic cluster of the resistant line is separated from other growth-enhanced commercial lines, providing a unique genomic signature of the genetic cluster of the resistant line. Lastly, having a unique genomic signature is a double-edged sword. On one hand, populations of other clusters can never overlap the resistant line no matter how many generations of selection take place. On the other hand, the resistant line will have a lower diversity (tight cluster) unless outside genetic material is introduced to the population. Currently, the legal requirements of defining a new aquaculture line consists of only field performance. For example, the Chinese government requires two years of culture data on 200,000-acre (13,333 ha) of water surface area that demonstrates improvement (Ministry of Agriculture and Rural Affairs of the People’s Republic of China, n.d.). Going above and beyond, most aquaculture companies now include experimental data and challenge data to present the characteristics of their lines, because the experimental design and hypothesis testing can pinpoint the improved characteristics. The acceptance of laboratory data is really facilitated by the growing number of companies and institutions that provide standardized experiments. Now, genomic selection brings FIGURE 2. Principle Component Analysis of shrimp SNP genotypes. The disease resistant population of the resistant line is genetically distinct from other commercial lines.