Optimization to the SCAR (Sequence Characterized Amplified Region) favors the isolation of polymorphic loci for phylogenetic studies in closely related taxa

Abstract

DNA sequence data have made a tremendous contribution to plant phylogenetics. Nonetheless, a notable shortcoming of several loci has been the poor phylogenetic resolution of relationships among closely related species. In this study a modifi cation to the SCAR method is proposed that consists of: a) digestion of polymorphic RAPD fragments instead of cloning them, b) sequencing of the digested fragments, and c) alignment of sequences for designing specifi c primers. This simple approach allowed us to fi nd variable DNA loci suitable for phylogenetic analysis at lower taxonomic
ranks.