Screening garlic EST sequences for SSR motifs

Abstract

SSR markers are one of the most preferable DNA molecular markers in plant genetic analyses because they are multi allelic, polymorphic, reproducible and transferable among the genetically close species although their development is costly and time consuming. Development of SSR markers can be accomplished with either sequencing of genomic library colonies containing SSR repeats or mining available sequences of related species in gene banks. The second method has been preferred in recent studies due to the dramatic increase in available nucleotide sequences of plant species. For garlic genome, limited SSR markers have been developed so far and development of more SSR markers is needed for detailed genetic characterization and mapping of garlic genotypes. In this study, we screened available garlic EST sequences for SSR motifs in order to generate EST-based SSR markers. We searched repeat motifs containing 2-6 nucleotides. The minimum repeat units criteria was ten for dinucleotides, seven for trinucleotides, five for tetranucleotides, and four for pentanucleotides and hexanucleotides. In total, 86 SSR motifs have been determined using these criteria and the most abounded repeat motifs were determined as (AT/TA)n. Primer pairs designed for some of these SSR motifs were observed as multi allelic and polymorphic among the garlic clones.