TMPD

BACKGROUND: Simple sequence repeats (SSRs) are tandem repeats of DNA that have
been used to develop robust genetic markers. These molecular markers are powerful
tools for basic and applied studies such as molecular breeding. In the model
plants in Nicotiana genus e.g. N. benthamiana, a comprehensive assessment of SSR
content has become possible now because several Nicotiana genomes have been
sequenced. We conducted a genome-wide SSR characterization and marker development
across seven Nicotiana genomes. RESULTS: Here, we initially characterized
2,483,032 SSRs (repeat units of 1-10 bp) from seven genomic sequences of
Nicotiana and developed SSR markers using the GMATA(R) software package. Of
investigated repeat units, mono-, di- and tri-nucleotide SSRs account for 98% of
all SSRs in Nicotiana. More complex SSR motifs, although rare, are highly
variable between Nicotiana genomes. A total of 1,224,048 non-redundant Nicotiana
(NIX) markers were developed, of which 99.98% are novel. An efficient and uniform
genotyping protocol for NIX markers was developed and validated. We created a
web-based database of NIX marker information including amplicon sizes of alleles
in each genome for downloading and online analysis. CONCLUSIONS: The present work
constitutes the first deep characterization of SSRs in seven genomes of
Nicotiana, and the development of NIX markers for these SSRs. Our online marker
database and an efficient genotyping protocol facilitate the application of these
markers. The NIX markers greatly expand Nicotiana marker resources, thus
providing a useful tool for future research and breeding. We demonstrate a novel
protocol for SSR marker development and utilization at the whole genome scale
that can be applied to any lineage of organisms. The Tobacco Markers & Primers
Database (TMPD) is available at http://biodb.sdau.edu.cn/tmpd/index.html.

Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana.

TMPD (The Tobacco Markers &amp; Primers Database) is a web-based primer database consisting of a simple sequence repeat (SSR) markers of Nicotiana.

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