Developmet of Universal SNP chips for Pacific White Shrimp

Pacific white shrimp is the most important species in shrimp aquaculture, making up the majority of the US$6.5 Billion worth of farmed shrimp imported into the US in 2017. The dominance of this species in shrimp aquaculture is due to the development of domesticated strains and years of continuous genetic improvement. Recent advancements in genome selection allow faster and more accurate selection of important traits, and the implementation of this technology is recently acknowledged in Pacific White Shrimp. To implement genomic selection, a high throughput genotyping of a massive number of SNPs is required. A commercial SNP chip is now available for Pacific White Shrimp. However, this SNP chip was developed from captive stocks with narrow genetic diversity, and may not be effective for stocks of different origins. This proposed project aims to develop universal SNP chips, derived from wild stocks across the geographic range of the species, and can therefore be used in any breeding program. The proposed SNP chips will have densities ranging from 14,000-50,000 loci, discovered using genotyping by sequencing. SNP frequencies will be compared between populations in order to screen for informative SNPs. In the commercialization step, the list of informative SNPs that can be applied on the solid-state SNP genotyping array could be designed for specific applications such as identifying stock origin, predicting genomic breeding values in domesticated lines of known origin, or investigating genome-wide association study. These designed SNP chips can be sold as products. In addition, Infini-SEA can provide consulting services on genome selection to Pacific White Shrimp breeding companies, using the developed SNP chips to evaluate the genomic prediction.