This collaborative multi-disciplinary research project will develop resources for functional, comparative, and evolutionary genomics of the Compositae, particularly lettuce (Lactuca sativa) and sunflower (Helianthus annuus). Six domestication and ten escape and naturalization events are being investigated to elucidate the genetic bases and evolutionary forces underlying the domestication of crops and evolution of weeds. These data will build on the Compositae Genome Project (CGP, http://compgenomics.ucdavis.edu) as well as capitalize on the wealth of knowledge being developed for Arabidopsis and other model species. Specifically, (i) 450,000 EST sequences will be deposited in GenBank and the CGP web site with an emphasis on allelic diversity (covering 18 plant species); (ii) the study of phenotypic and molecular variation in seven genera is being examined for patterns of selection and sequence or expression differences associated with domestication or weed traits, (iii) quantitative traits and gene expression patterns for seed oil profiles in lettuce and sunflower are being detected, and (iv) gene order and chromosome rearrangements in lettuce, sunflower, and Arabidopsis are being characterized. This research will investigate a broad range of genes involved in evolution of cultivated plants and weeds and will evaluate of the relative importance of changes in gene sequence versus changes in gene expression for the evolution of different traits such as flowering time, seed production and quality and clonal growth among others. The genetic bases of parallel evolutionary trends (e.g. changes to short life cycles, or changes from annual to perennial growth) will be assessed and will provide a basis for future functional analyses. The data and resources developed with this project will be readily available to the scientific community through the CGP web site and commercial distributors of clones and arrays. Multiple national and international interactions with the academic and private sectors will allow for rapidly released agriculturally useful information and genetically diverse accessions. Our project is complementary to downstream programs in the private sector. The CGP will have significant economic impact and generate permanent resources for the Compositae, one of the largest and ecologically successful families. Lettuce is one of the top ten US crops and sunflower ranks #14 worldwide. The family also includes many minor crops, important weeds, and species with novel biochemistries. The CGP funnels basic genomics information to crop improvement by efficiently leveraging information from the sequencing and functional genomics of model organisms. The project contributes to the genetic data being developed across all plants. The CGP emphasizes multidisciplinary teams with expertise drawn from multiple universities. The CGP integrates genetics, biochemistry, physiology, and bioinformatics and will provide broad training in these areas. In addition, an effective outreach program that impacts all levels of students is in place. The CGP will provide research experience to minorities, especially at Cal Poly Pomona and U. Mass., Boston and introduce computer science majors to biology.
