Abstract:This study aimed to develop a universal genotyping tool for common salmonid species cultured in China. Using an Affymetrix rainbow trout (Oncorhynchus mykiss) 57 K single nucleotide polymorphism (SNP) array, four representative aquaculture salmonid populations were genotyped, including Oncorhynchus masou masou, Oncorhynchus kisutch, Salvelinus fontinalis, and Salvelinus leucomaenis. A total of 96 shared polymorphism markers was screened out of 57,501 SNPs, then a low-density SNP array was constructed based on a Fluigidm 96.96 dynamic array, which is universal for the genera Oncorhynchus and Salvelinus. Reliability of the genotyping results was high because the identity of results with those of the Affymetrix 57 K array reached 96.55%. Parentage assignment for 48 Oncorhynchus kisutch offspring was performed with Cervus 3.0.7 software, based on genotyping data by the 96 SNP array. The results matched perfectly with the true pedigrees among complicated families, proving high accuracy in the pedigree assignment application of the 96 SNP array. The non-exclusion probability for the first parent (NE-1P) was 4.120×10–4 during single parent assignment, whereas the non-exclusion probability for the parent pair (NE-PP) was as low as 6.219×10–12. Genetic structure analysis for four salmonid populations was also performed using genotyping data of the 96 SNP array. Clustering results were in accordance with the taxonomic categories of the samples, whereas certain degrees of genetic introgression were observed among the populations, indicating that the genetic composition and relationships among populations were properly demonstrated in the analysis. All these results suggested that the developed 96 SNP array has great potential in genetic analyses for salmonid populations, which might provide helpful genome-wide information for plasm resource evaluation, selective breeding, high-quality fry production, and reasonable foreign strain introduction in the Chinese salmonid aquaculture.
