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 1b Summary of the success of candidate SNP loci identification with different priming approaches in (b) other salmonids.

	PCR primer design strategy
Process description	EPIC I ^a	EPIC II ^b	IPEC ^c	Total
T. thymallus
No. loci tested	22	-	20	42
No. loci producing clear PCR product	11 ^d		4	16
No. loci successfully sequenced	4	-	2	5
No. polymorphic loci	3	-	2	5
S. trutta
No. loci tested	-	-	10	10
No. loci producing clear PCR product	-	-	8	8
No. loci successfully sequenced	-	-	6	6
No. polymorphic loci	-	-	4	4
S. alpinus
No. loci tested	-	-	10	10
No. loci producing clear PCR product	-	-	5	5
No. loci successfully sequenced	-	-	3	3
No. polymorphic loci	-	-	1	1

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 six loci either produced a smear or no amplification was observed

ISSN: 1471-2164