AFLP-SSCP: A Useful AFLP-Based Method for Informative SNPs Discovery in Non-Model Organisms

Abstract

Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation among individuals of a species. Recently, in spite of the development of high-throughput genotyping technologies, SNPs have been applied as markers for population genetic and high-density genetic mapping. However, the high costs of SNPs discovery and genotyping assay limit the applications of SNP markers in non-model organisms. In this study, we present a cheap and convenient AFLPbased (Amplified fragment length polymorphism) strategy that is highly efficient for developing informative SNP markers without any prior information. We developed SNP markers in a nonmodel and economic aquaculture species Asian Seabass (Lates calcarifer), and discussed the potential use of the combinations of AFLP and AFLP-SSCP.