Simple Sequence Repeat (SSR) Marker Development

We are developing genetic markers for several uses. The people from NSF-funded Missouri Maize Project, who are really good at SSR development, are helping us. They have identified 261 unique SSR loci from Nicotiana sequences currently in GenBank, and designed primers for amplifying them. So far, about 40% of these have been useful, i.e. they amplify well, produce interprettable banding patterns, and are genetically variable.

We also have many published sources for SSR loci, including 40 from the Nicotiana chloroplast genome (Bryan et al., 1999, Theor. Appl. Genet. 99:859), 80 from Lycopersicon (Smulders at al., 1997, Theor. Appl. Genet. 97:264-272), 89 from Solanum (Milbourne et al., 1998 Mol. Gen. Genet. 259:233-245) and 92 nuclear SSRs from Nicotiana (pers. comm. from M.J.M. Smulders; many of these are probably also included in the 261 loci that the maize people found for us.

A table of candidate SSR loci in .pdf format is here.

Applications for the SSR loci include:

• Systematics of the 7 closely-related species in Nicotiana Section Alatae. DNA sequence information from nrITS and cp tRN-L intron have not been sufficient to tease apart these relationships so the SSR allele frequencies will be used to estimate a distance-based phylogeny.
• QTL-mapping. We hope to follow the evolution of floral traits, that we have demonstrated at the phenotypic level, at the DNA level. The first step toward this goal is to find SSR loci that are in linkage disequilibrium with the floral traits. These QTL, along with a sample of non-QTL markers (as controls for drift and selection on unmeasured traits), will be assayed in populations that were produced by natural pollination (mostly by hawkmoths, some hummingbirds) versus populations that share the same ancestry and selection regimes but were produced by hand pollinations among randomly-chosen plants.
• Population genetics: SSR markers will be used to quantify genetic structure of populations and gene flow within and among species.

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