SSR Discovery in Common Dandelion (Taraxacum officinale) from EST Sequence Databases

Microsatellites or SSRs (simple sequence repeats) are short tandem duplications randomly distributed in eukaryotic genomes. SSR markers derived from genomic sequences have greatly improved marker assisted selection (MAS) for plant breeding. Database screening provides the most readily available approach to search SSRs. The availability of expressed sequence tags (ESTs) in the public databases has resulted in the development of the genomic markers named EST-derived SSR (EST-SSR) markers. Generally, traditional markers used in genetic diversity study are derived from the non-coding regions of the genome. However, EST-SSR markers detect the true functional region of the genome thus determine the genetic diversity of the coding regions of the genome. The objective of this study was to discover SSRs in the EST database that are available in NCBI for common dandelion (Taraxacum officinale). SSRLocator, Blast2Go and DNASTAR were used for data mining. As a result, there were 6,283 non-redundant EST (NR-EST) sequences from 41,295 redundant EST sequences. Only 572 NR-EST (9.1%) sequences contained SSR and a total of 607 SSRs with different motifs were found in T. officinale EST sequences. Within these EST-SSRs, 52.2%, 21.6%, and 23.2% showed monomeric, dimeric and trimeric motifs, respectively. Only about 3% of the sequences showed tetrameric, pentameric and hexameric SSR motifs. PCR primers were designed for the 607 SSRs and virtual-PCR was simulated using SSRLocator. In addition, these NR-EST containing SSRs were categorized based on Gene Ontology (GN) regarding molecular function, biological processes and cellular components. Validation of SSR primers is in progress using five different T. officinale collections. This study provides the preliminary bioinformatics information for MAS using SSR markers in dandelion breeding.