Poster: Comparative Genomics

Abs # 925: A method for physically mapping the genomes of Oryzeae species using "overgo" probes from rice chromosome 1

Presenter:	Hass, Barbara L., bhass@purdue.edu
Authors	Hass, Barbara L. (A)   Westerman, Rick  (A)   SanMiguel, Phillip  (A)   Jackson, Scott A. (A)
Affiliations:	(A): Purdue University

Comparative genomics is becoming increasingly important for the characterization of gene function and for the study of chromosome evolution. While projects to sequence a number of genomes have been undertaken, little or no sequence data exists for the majority of species. In order to ascertain the evolution of genomes of related species over time, methods are needed to exploit the known sequence data to rapidly and efficiently identify homologous regions in genomes which have not been fully sequenced. To that end, we are using "overgo" technology to design probes, using published sequence data from rice chromosome 1, to screen BAC libraries from O. sativa and five other Oryzeae species. Positive BAC clones from these screens will be fingerprinted and assembled into contigs, which can then be studied to determine the colinearity of regions of rice chromosome 1 among rice and other species. 1182 overgos, covering 9 contigs, have been designed so far. 48 of these overgos were combined into 6 pools and used to probe replicate slot blots containing genomic DNA from 10 rice species, wild rice, maize, and sorghum. Each pooled probe consisted of 8 adjacent overgos spanning an approximately 200kb region. All of the rice species were positive for each pool, and at least one pool produced a positive hybridization signal in maize, wild rice, and sorghum. In addition, 96 overgos, arrayed in a 96-well format, have been pooled by row and by column and, and these pools used to probe a rice BAC library. These preliminary screens have resulted in the identification of a number of positive clones. These BACs will be rearrayed and screened a second time to confirm which clones correspond to each overgo sequence before they can be fingerprinted and contigs assembled.