Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

Translating Genome Sequence Resources Into Applied Outcomes In The Solanaceae: The Vision Of SolCAP.

David Francis¹ , David Douches² , Walter De Jong³ , Shanna Moore³ , Allen Van Deynze⁴ , C. Robin Buell² , Esther van der Knaap¹ , Matthew Robbins¹ , Sung-Chur Sim¹

¹  The Ohio State University/OARDC, Wooster, OH 44691

²  Michigan State University, East Lansing, MI 48824

³  Cornell University, Ithaca, NY 14853

⁴  University of California, Davis, CA, 95616

Data from expressed sequence tags and from whole-genome sequencing has opened opportunities for experimentation and application in the Solanaceae. These resources are also driving agricultural research toward a perspective that emphasizes taxonomic groups and DNA sequence homology rather than traditional commodity boundaries. The long-term objective of the Solanaceae Coordinated Agricultural Project (SolCAP) is to provide infrastructure to link allelic variation in genes for valuable traits in the three most important vegetable crops in the Solanaceae: potato, tomato and pepper. Leveraging resources between commodities has resulted in tools to manipulate phytonutrient biosynthesis pathways affecting potato tuber and tomato fruit nutritional quality. Strategies to develop Single Nucleotide Polymorphisms (SNPs) as molecular markers for whole-genome analysis include analysis of polymorphisms in EST databases, hybridization to oligonucleotide arrays to detect single feature polymorphisms (SFPs), and de novo sequencing using ultra-high throughput techniques. Application of SNPs has emphasized genotyping of core collections of varieties representing different stages in the domestication process, different market classes, and regional adaptation. Wild species accessions are also included in the core collections as out groups. A variety of indexes and clustering procedures were used to analyze population structure within the cultivated germplasm, and the results have implications for crop improvement efforts. By extending sequence resources horizontally to encompass both accessions of wild relatives and populations of elite varieties, a greater understanding of how variation in DNA sequence affects variation in phenotype is expected.