Targeted SNP discovery in Atlantic salmon (Salmo salar) genes using a 3'UTR-primed SNP detection approach

BMC Genomics

Table 1 Summary of success rates when testing two strategies for SNP discovery in a set of target genes

SNP discovery strategies tested:	3'UTR-primed SNP discovery approach	*in silico* SNP mining approach
Number of genes (cCDS-FLIcs) tested	208	168
candidate SNPs success rate¹	-	0.82 (131/168)
Initial PCR and sequencing success rate²	0.79 (165/208)	0.47 (61/131)
SNP discovery rate³	0.45 (74/165)	0.41 (25/61)
SNP discovery success rate⁴	0.36 (74/208)	0.15 (25/168)

¹Number of target genes with at least one putative SNP/total number of target genes selected for testing the in silico SNP mining method. ²Number of primer pairs producing PCR fragments suitable for sequence analysis/total number of primer pairs tested. ³SNP discovery rate: one or more SNP discovered/PCR fragments analysed in the small population materials. ⁴SNP discovery success rate: genes with at least one SNP discovered/total number of genes tested.

ISSN: 1471-2164