Single nucleotide polymorphism (SNP) discovery in duplicated genomes: intron-primed exon-crossing (IPEC) as a strategy for avoiding amplification of duplicated loci in Atlantic salmon (Salmo salar) and other salmonid fishes

Table 1a Summary of the success of candidate SNP loci identification with different priming approaches in (a) Atlantic salmon.

	PCR primer design strategy
Process description	EPIC I ^a	EPIC II ^b	IPEC ^c	Total
S. salar
No. loci tested	22	25	22	69
No. loci producing clear PCR product	13 ^d	1 ^e	21	36
No. loci successfully sequenced	4	6	17	27
No. polymorphic loci	0	3	8	11

a – primers in exons of salmonid genes
b – primers in exons of other teleost genes
c – at least one primer in intron regions of salmonid genes
d – in five loci two distinct PCR bands were observed and four loci produced a smear
e – most of the primers produced several PCR bands and thus re-amplifications were needed (see Methods)

ISSN: 1471-2164