Plant & Animal Genomes XI Conference Plant & Animal Genomes XI ConferenceJanuary 11-15, 2003
Town & Country Convention Center
San Diego, CA
Workshop: Compositae
The Compositae Genome Project (http://compgenomics.ucdavis.edu/) aims to determine the genetic linkage relationships and molecular bases of metabolic and morphological changes associated with domestication of lettuce and sunflower. The initial phase of this project is complete. Over 60,000 lettuce and 40,000 sunflower ESTs have been sequenced from multiple cDNA libraries from two genotypes of each species. Libraries were generated using a tagging and pooling strategy to maximize the diversity of genes sequenced. Post sequencing deconvolution based on tags incorporated into the primers was used to determine tissue sources of ESTs. ESTs have been assembled using the CAP3 program. These assemblies represent ~19,000 lettuce and 12,000 sunflower unigenes. Computational approaches and comparison with Arabidopsis orthologs suggested that ~2% of the contigs were misassembled chimeras. Comparisons with Arabidopsis indicated about 10% of the contigs could be assembled further. ESTs have been assigned to broad functional classes and their expression levels in the different source tissues determined. Candidate genes for agriculturally important traits are being identified and mapped. A new approach has been implemented to identify polymorphisms between the parents of the mapping populations. About 250 INDELs and 2,500 SNPs have been discovered for lettuce and sunflower. These have been confirmed in wet lab analysis in ~90% cases and we are in the process of mapping them in a high throughput manner. About 1,200 lettuce and 500 sunflower putative COS (conserved ortholog set) markers have been identified based on clustering with the complete Arabidopsis genome. These are also being mapping for analysis of synteny.