Project Number: 3655-21000-050-04
Project Type: Specific Cooperative Agreement

Start Date: Aug 01, 2008
End Date: Jul 31, 2009

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:
420 COSII will be mapped in a reference population of potato. Emphasis will be given to the tomato/potato inverted regions, and to QTL regions for domestication and resistance traits across Solanaceae. SNPs and indels identified in the above sequencing of 420 COSII will be mapped in a reference population of potato as CAPs, SSCP or simple PCR, using the most informative progeny subset and ordered using IntiMap software. Scoring will be extended to the full mapping population of >100 individuals, once reliable polymorphisms are detected and position preliminarily assigned. JoinMap software version 3.0 will be used for linkage analysis and map calculations to develop a consensus of both parental maps. We will also recover and compile raw data supporting prior publications from genetic and QTL mapping using this population.