SNPs by AFLP (SBA): a rapid SNP isolation strategy for non-model organisms.

Despite the great potential of single nucleotide polymorphism (SNP) markers in evolutionary studies, in particular for inferring population genetic parameters, SNP analysis has almost exclusively been limited to humans and 'genomic model' organisms, due to the lack of available sequence data in non-model organisms. Here, we describe a rapid and cost effective method to isolate candidate SNPs in non-model organisms. This SNP isolation strategy consists basically in the direct sequencing of amplified fragment length polymorphism bands. In a first application of this method, 10 unique DNA fragments that contained 24 SNPs were discovered in 11.11 kb of sequenced genomic DNA of a non-model species, the brown trout (Salmo trutta).