Development of a global SNP resource for diversity, provenance, and parentage analyses on the Indo-Pacific giant black tiger shrimp (Penaeus monodon)

The giant black tiger shrimp (Penaeus monodon) is an important aquaculture and fishery species and is the second most farmed penaeid shrimp species globally. Genomic resources available in giant black tiger shrimp research are growing rapidly. However, considering the large number of animals that would require SNP genotyping for commercial applications (i.e., selective breeding programs), there is a commercial need to identify low-density SNP panels for rapid, robust, and cost-effective use in global diversity, provenance, and pedigree determination. Using the raw (n = 131,929 SNPs) and high-quality (n = 10,593 SNPs; Vu et al., 2021) datasets, five low-density panels were identified for the standardized determination of: (1) global diversity (n = 2155 SNPs), (2) global provenance (n = 1200 SNPs), (3) Pacific Ocean (PO) pedigree (n = 217 SNPs), (4) Sri Lanka (SLK) pedigree (n = 226 SNPs), and (5) West Indian Ocean (WIO) pedigree (n = 220 SNPs). A total of 3433 unique genome-wide SNPs comprise these five low-density panels. Genetic diversity simulations demonstrated that the global diversity panel was able to estimate unbiased genetic diversity within and among all Indo-Pacific P. monodon populations as accurately as the entire highquality dataset (n = 10,593 SNPs). Both DAPC and NetView analyses demonstrated that the global provenance panel was able to trace P. monodon collected from the same region back to their original basin and genetic cluster, while Monte-Carlo tests demonstrated that individuals could be accurately assigned back to their original basin, region, and basin-specific sampling location with 100%, 100%, and 69–100% accuracy, respectively. In silico analyses demonstrated that the PO, SLK, and WIO pedigree panels were able to accurately assign theoretical progenies back to their parent-pair with 100% accuracy using only 30–40 of the most informative SNP markers. This study provides globally effective and accurate low-density SNP panels for Indo-Pacific P. monodon, which can help aquaculture practices and fishery management strategies through improved diversity, provenance, and pedigree determination as well as facilitation of global data consistency, global database development, and global analysis standards establishment