CoPIs: Scott A. Jackson (Purdue University), Manyuan Long (University of Chicago), Carlos A. Machado (University of Maryland), and Michael J. Sanderson (University of Arizona)
Collaborators: O. Panaud (University of Perpignan, France) and D. Weigel (Max Planck Institute for Developmental Biology, Germany), Doreen Ware (Cold Spring Harbor Laboratory), Qifa Zhang and Sibin Yu (Huazhong Agricultural University, China), Bin Han (National Center for Gene Research, China), Marco Wopereis (Africa Rice Center (WARDA), Benin), Mathias Lorieux (International Center for Tropical Agriculture (CIAT), Columbia, and Georgia Eizenga (DB NRRC, Germany.
Intellectual merit. Asian cultivated rice (Oryza sativa) feeds more people than any other crop. As the rice-dependent population is expected to double in about 25 years, breeders are faced with the enormous task of doubling rice yields with less land, water, and fertilizers, and on poorer soils. It is therefore critical that the scientific community unites to provide the tools and biological/evolutionary insights required to meet future needs. The project's long-term goal is to exploit 15 million years of evolutionary diversification and adaptation that have been locked in the genomes of wild and domesticated Oryza species, to both improve cultivated rice and address fundamental questions in evolutionary and comparative genomics. To accomplish this goal the project will first generate a set of publicly available genomics resources for the genus Oryza including: i) physical maps for three wild relatives of cultivated rice and the closely related outgoup species Leersia perrieri; ii) complete sequences for the short arms of chromosome 3 of these species; iii) complete reference genome sequences for O. barthii (the wild progenitor of West African cultivated rice), and O. punctata (a wild species that will serve as the evolutionary outgroup the eight AA genome species--the species group containing O. sativa); iv) gene and small RNA expression data sets for 11 Oryza species and L. perrieri; and v) DNA polymorphism data sets across the AA genome phylogeny. The project will integrate these new resources with 5 to 8 forthcoming new Oryza reference genome sequences to create the most comprehensive within-genus comparative genomics platform for any plant system. The project will interrogate this comparative genomics platform to discover key evolutionary events and characterize the forces that led to the formation of 24 Oryza species with 10 different genome types. Specific research areas that will be addressed include: analyses of structural variation, phylogenomics, population genomics, genome evolution and the origin of new genes, and the role of transposable elements in genome evolution. Libraries, genome sequences and their annotations will be accessible via public databases and repositories, such as the AGI BAC/TEST Resource Center (www.genome.arizona.edu/orders/), NCBI (www.ncbi.nlm.nih.gov/), and Gramene (www.gramene.org).
Broader impacts. This project will have broad impacts at several levels, including basic and applied research communities, postdoctoral/graduate/undergraduate and high school student training and mentoring, community outreach, and K-5 children and their families. For basic/applied research communities, the project will enhance and develop a genus-level resource as a platform for accessing new traits and alleles that is unparalleled in the plant world. This transformative platform can be used to address fundamental hypothesis-driven questions as well as provide essential tools to improve the world's most important food crop. The project will provide training and mentoring to postdoctoral scientists, graduate/undergraduate students and high school students interested in genome evolution, plant breeding, and careers in academic and corporate science. Finally, the project will develop a biannual "Plant Science Family Night" program, targeting K-5 students and families, to get children and their families excited about plants and the role plant science plays in ensuring a safe, sustainable, and secure food supply for our planet.
