Project Number: 3655-21000-050-05
Project Type: Specific Cooperative Agreement

Start Date: Sep 02, 2008
End Date: Feb 28, 2010

Objective:
To enhance understanding of and access to the genetic diversity in wild and landrace relatives of tomato and potato, and contribute to the same for other euasterid plant species, five objectives are proposed: 1. Document relative diversity in and relationships among a core germplasm set of wild and cultivated tomato and potato species as revealed by DNA sequences of COSII genes. 2. Help orient the utilization of tomato and potato diversity by re-evaluating grouping concepts based on unbiased measures given by COSII markers. 3. Identify and describe putative regions of positive and negative selection throughout tomato and potato genomes and relate these to known domestication loci or mapped phenotypic traits, focusing on COSII markers linked to domestication loci (Appendix 1). 4. Facilitate comparative mapping in the Solanaceae by mapping 300 single-copy COSII (to include the 48 above) in potato, lulo, sweet potato, and carrot. 5. Make these data publicly available on the SGN bioinformatics platform (http://sgn.cornell.edu/).

Approach:
The Sol Genomics Network (SGN) will generate primers, experimental conditions, and sequence for the 24 COSII markers in this study, and up to the same number of sequences from mapping parents of each of three other crop species in the Euasterid II clade. In addition, marker sequences, experimental conditions, and polymorphism information will be stored in the SGN database and a web query interface provided. The maps generated will be added to the SGN mapping database and available through the SGN comparative mapviewer. With this viewer, different genetic maps in the SGN database can be compared dynamically. The newly developed maps will therefore be available for comparison with tomato, pepper, eggplant, and Arabidopsis. Trees and alignments will be shown through our tree-browser and alignment viewer software. We will also create a special SGN portal that will contain introductions to SGN features and COSII for a breeder's perspective on the best utility of the data deposited at SGN.