PI: Rod A. Wing (University of Arizona) Co-PIs: Scott A. Jackson (Purdue University), Steven D. Rounsley (University of Arizona), Lincoln D. Stein (Cold Spring Harbor Laboratory)
Comparative genomics is a powerful tool to understand how genes and genomes function and evolve yet limited studies have been done comparing the genomes of species within a genus. Such comparisons are critical for a deeper understanding of speciation, polyploidization, domestication and gene regulation. The two most advanced genus level comparative systems available for higher eukaryotes are the Drosophila comparative genome sequencing project where 12 wild Drosophila genomes are being sequenced, assembled and compared to the reference D. melanogaster genome, and the Oryza map alignment project (OMAP) were physical maps of 12 wild rice genomes have been made and aligned to the reference O. sativa genome.
The long term goal of this project is to create a freely available comparative sequence resource with broad utility that can be interrogated to ask fundamental questions in genome biology, evolution and domestication in the genus Oryza. To accomplish this goal, BAC tiling paths of the short arm of rice chromosome 3 across three diploid genomes (AA, BB and CC) and their allotetraploid progeny (BBCC) will be sequenced and rigorously annotated.
The sequence generated from this project will have broad utility to the scientific community in the following ways:
1) The sequence will provide comparative information on all genes and transposable elements that are common between the AA, BB, CC, BBCC genomes (e.g. allelic diversity, conserved non-coding sequences).
2) The sequence will permit the identification of genes and transposable elements that are unique to cultivated rice as well as to the other wild species. For cultivated species, the unique genes may play important roles in domestication and would be prioritized for functional analysis. With respect to the wild rice accessions, the unique genes may play important roles for survival and adaptation to particular environments where they originated.
3) The sequence will also provide an unprecedented data set in regions of the short arm of chromosome 3 that have undergone rearrangements (e.g. insertions, deletions, inversions and translocations). By integrating these rearrangements with genetic maps we will be able ask fundamental questions on the role that rearrangements, expansions and contractions play in chromosome speciation, genome size maintenance and the evolution of new genes.
In addition to the scientific broader impacts of this proposal, a summer genomics outreach training program will be offered targeting under-represented college students and faculty to apply and extend knowledge gained in the classroom to practical experience. Students will have the opportunity to view careers in biology and will be encouraged to continue their education through the M.S. and Ph.D. levels. Interns will participate full-time in a PI lab during eight-week summer sessions. Each student will be paired with a mentor who will help develop a research project that is in alignment with the intern's particular area of interest and expertise.
Access to project outcomes Project outcomes will be available in the form of publications in peer-reviewed journals and the Gramene public cereal database (www.gramene.org). All sequence and trace file data will deposited in Genbank (www.ncbi.nlm.nih.gov/).
