TMPD

TMPD provides a centralized database of simple sequence repeat (SSR) markers and primers for Nicotiana species to support genome-wide marker discovery, genotyping, and molecular breeding in tobacco research.

Key Features:

• Genome-wide SSR characterization: Genome-wide identification and characterization of simple sequence repeats (SSRs) of 1–10 bp across seven Nicotiana genomes.
• SSR catalogue size: A total of 2,483,032 SSRs were identified, with mono-, di-, and tri-nucleotide repeats constituting 98% of detected SSRs.
• Complex motif variability: More complex SSR motifs, though rarer, exhibit significant variability across different Nicotiana species.
• NIX markers: Development of 1,224,048 non-redundant Nicotiana (NIX) markers, with 99.98% reported as novel.
• Amplicon information: Amplicon size data for alleles are provided for each genome.
• Marker development software: Marker development conducted using the GMATA® software package.
• Validated genotyping protocol: An efficient and uniform genotyping protocol has been validated for use with the SSR markers.
• Marker utility: SSR markers characterized for high variability and applicability in molecular breeding and genetic studies of Nicotiana.

Scientific Applications:

• Marker discovery and primer design: Support for identifying SSR loci and associated primers for downstream genotyping experiments.
• Genetic diversity and population studies: Use of SSR markers to assess variability and population structure across Nicotiana species.
• Molecular breeding and marker-assisted selection: Deployment of SSR markers and NIX markers in breeding programs for trait mapping and selection.
• Genotyping and allele sizing: Allele amplicon size information enables genotype scoring and comparative allele analysis.
• Comparative genomics: Comparative assessment of SSR content and motif distribution across seven Nicotiana genomes.

Methodology:

Genome-wide identification and characterization of SSRs (1–10 bp) across seven Nicotiana genomes using the GMATA® software package for marker development, yielding 2,483,032 SSRs and 1,224,048 non-redundant NIX markers.