We are building a framework physical infrastructure across the soybean genome by using SSR (simple sequence repeat) and RFLP (restriction fragment length polymorphism) markers to identify BACs (bacterial artificial chromosomes) from two soybean BAC libraries. The libraries were prepared from two genotypes, each digested with a different restriction enzyme. The BACs identified by each marker were grouped into contigs. We have obtained BAC- end sequence from BACs within each contig. The sequences were analyzed by the University of Minnesota Center for Computational Genomics and Bioinformatics using BLAST algorithms to search nucleotide and protein databases. The SSR-identified BACs had a higher percentage of significant BLAST hits than did the RFLP-identified BACs. This difference was due to a higher percentage of hits to repetitive-type sequences for the SSR-identified BACs that was offset in part, however, by a somewhat larger proportion of RFLP-identified significant hits with similarity to experimentally defined genes and soybean ESTs (expressed sequence tags). These genes represented a wide range of metabolic functions. In these analyses, only repetitive sequences from SSR-identified contigs appeared to be clustered. The BAC-end sequences also allowed us to identify microsynteny between soybean and the model plants Arabidopsis thaliana and Medicago truncatula. This map-based approach to genome sampling provides a means of assaying soybean genome structure and organization.

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Xanthomonas oryzae pv. oryzae (Xoo) and X. oryzae pv. oryzicola (Xoc) are important bacterial pathogens of rice (Oryza sativa). Despite being very closely related, they infect in different ways and cause distinct diseases. Xoo invades the xylem to cause bacterial blight, whereas Xoc colonizes the leaf mesophyll to cause bacterial leaf streak. As the modes of infection of these two pathogens are different, traditional methods of inoculation effective for Xoo are not effective for Xoc and vice versa. We discovered that dipping plants in bacterial suspension is an effective inoculation method both for Xoo and Xoc and can be used to achieve uniform and synchronized infection of multiple plants. Using this method, comparable sets of rice Gateway Ò cDNA libraries spanning five time points in the early stages of bacterial blight and bacterial leaf streak were constructed. Prepared under identical conditions, the libraries are ideal for probing differential rice transcription during development of the diseases. Furthermore, by capturing transcripts expressed in response to these unique sources of biotic stress, the libraries are likely to contain cDNA clones not available elsewhere.www.blackwell-synergy.com