Comparative Genomics of Phenotypic Variation in the Compositae

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PI: Loren Rieseberg (Indiana University)CoPIs: Richard Michelmore and Kent Bradford (University of California ? Davis), Richard Kesseli (University of Massachusetts - Boston), John Burke and Steven Knapp (University of Georgia), David Still (California State Polytechnic University - Pomona)Senior Personnel: Zhao Lai (Indiana University)The Compositae (also known as the Asteraceae) is one of the largest, most diverse, and most economically important plant families. While lettuce, sunflower, and safflower are the three most valuable members of this family, over 40 species have been domesticated for a wide variety of uses. The Compositae also contains some of the world's most noxious weeds, which cost the United States an estimated $35 billion annually. The primary goal of this project is to develop genomic resources for the continued study of this important plant family. This work will include: (i) sequencing the gene-rich regions of the lettuce, sunflower, and safflower genomes; (ii) generation of "gene catalogs" for 25 additional taxa, including six crops, three weeds, the wild progenitors of ten crops and weeds, representatives of five taxonomically important subfamilies within the family, and an outgroup (i.e., a close relative of the family); (iii) analyses of the prevalence of variation in gene copy number versus nucleotide variation; (iv) analyses of the effects of whole genome duplications on diversification rates within the family; (v) identification of parallel genetic changes across crop/weed lineages; (vi) construction of ultra-high density genetic maps of lettuce, sunflower, and chicory; (vii) development of permanent populations for genetic mapping in key Compositae species; and (viii) the identification and validation of candidates for genes underlying important crop- and weed-related traits. This research will result in the generation of permanent resources for the Compositae research community and will have a significant economic impact through its contributions to both crop and weed science. This project will also result in the training of students at all levels in genetics, biochemistry, physiology, comparative genomics, and bioinformatics.Broader Impacts This project will have a major, lasting impact on both crop and weed science through the production of permanent, publicly available genomics resources. All results will be disseminated via publication in peer-reviewed journals, presentations at national and international meetings, and the resulting data will be made publicly available through the project website (http://compgenomics.ucdavis.edu) and via deposition in GenBank and other freely-accessible, online databases. In addition, all resulting germplasm resources will be freely distributed to interested parties upon request. This project also has a significant outreach component. Not only will it directly support multiple postdoctoral researchers, graduate students, and undergraduates, but it will also contribute to the training of many others, including high school interns. Outreach efforts will be specifically targeted at members of traditionally underrepresented and/or disadvantaged groups. Minority-serving institutions California State Polytechnic University - Pomona and the University of Massachusetts - Boston will serve as feeder institutions for identifying and placing minority student in collaborating labs. Outreach efforts on all participating campuses will also leverage existing, local programs to ensure maximum effectiveness. Project members will also interact directly with colleagues who are developing a plant genomics workshop to train high school teachers. Finally, this project will result in the production of a plant genomics text suitable for advanced undergraduates and/or graduate courses.