Project Number: 3655-21000-050-01
Project Type: Reimbursable

Start Date: Mar 01, 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:
USDA and Univ. Wisconsin (Ane) activity. Assessment of genetic and allelic diversity and phylogenetic relationships, with 24 COSII (four per linkage group), across 59 individuals to include cultivated and wild tomato and potato species and outgroups, and a nested diversity assessment in tomato and potato. All of the sequencing will be with a single individual per accession except for a nested study inside the S. peruvianum/S. brevicaule study that will use five clones of each of five individuals for five accessions of S. peruvianum and five clones for five individuals of five accessions in the S. brevicaule complex. The USDA will also sequence parents of one potato mapping population for the 420 COSII markers to be placed on the potato linkage map, and the mapping parents of lulo, sweetpotato and carrot to be provided by cooperators, for their inclusion in diversity and phylogenetic assessment. Some of these species will be the same as those used in the potato AFLP and SSR studies as mentioned above for comparative diversity assessments. CIP activity. 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. Cornell Univ activity. Database and bioinformatics. 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.