SNP Arrays for Species Identification in Salmonids.

The use of SNP genotyping microarrays, developed in one species to analyze a closely related species for which genomic sequence information is scarce, enables the rapid development of a genomic resource (SNP information) without the need to develop new species-specific markers. Using large numbers of microarray SNPs offers the best chance to detect informative markers in nontarget species, markers that can very often be assayed using a lower throughput platform as is described in this paper.

Identification of multiple diagnostic SNP loci for differentiation of three salmonid species using SNP-arrays.

This paper reports the use of SNP-array technology in a cross-species study for non-ambiguous species identifications. Based on an existing SNP-array for Atlantic salmon (cross)hybridisations with samples of salmon, brown trout and rainbow trout were analyzed to identify species-specific diagnostic markers. In total 566 SNP loci were identified to be highly polymorphic across the three salmonid species providing the molecular basement for various monitoring applications in aquaculture and food industries.

Genotyping of two populations of Southern Baltic Sea trout Salmo trutta m. trutta using an Atlantic salmon derived SNP-array.

The sea trout (Salmo trutta m. trutta) is an anadromous, teleost fish species characterized by homing behaviour. The sea trout has considerable ecological and economic significance. It reproduces naturally in rivers flowing into, and is common in, the Baltic Sea. In Poland spawning aggregations occur in the Vistula River and the rivers of Pomerania. Two populations from the Vistula River (TW) and a Pomeranian river, the Slupia (TP) were mixed in the past by stocking. The main purpose of this study was an assessment of the applicability of the Atlantic salmon custom design Illumina iSelect SNP (Single Nucleotide Polymorphisms) array containing 15,225 markers for identification of genetic diversity between sea trout populations. A diagnostic panel of 39 SNPs with a mean FST=0.1298 was selected from a pool of 15,225. At each locus, minor allele frequency was higher than 0.01 and mean expected heterozygosity for TW and TP populations were 0.343 and 0.271 respectively. Individuals tested were clustered in one of two groups which corresponded to their origins where the TW population was genetically more homogenous (membership coefficients ranked from 88.8% to 98.6%) while the TP population was more diverse (membership coefficients ranked from 53.8% to 98.5%). The results demonstrated the applicability of the Salmon 15K SNP-chip for determining the differences between Southern Baltic populations of the sea trout, a closely related salmonid species.