¹ Clemson University Genomics Institute, Clemson, SC, 29634, USA, http://www.genome.clemson.edu

Rice (Oryza sativa),as a main staple food for more than half of the world’s population, it has many merits for genome study, such as its relatively small genome size (430Mb), the collinearity of its genes with other important cereal crops such as corn, barley, wheat, etc., and well-established genetic maps and transformation systems. Chromosome 10, the smallest among 12, is estimated to be 20Mb in size based on RGP's YAC physical map which contains three gaps. Sequencing of chromosome 10 has been initiated by the CCW consortium (Clemson University Genomics Institute, Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center) and TIGR (The Institute for Genome Research). We focused on a 3.9cM region of chromosome 10p0.0-p3.9. CUGI fingerprinting contigs in this region were selected primarily by nine RFLP marker anchoring. The contiguous physical map, which covers 2.2Mb was completed using STC derived overgo hybridization. 15 minimal overlapping BACs were selected based on the sequence tagged connector (STC) extension method among 423 clones in the final physical map. Shotgun libraries of those BACs were constructed with high throughput strategy, then sequenced, and assembled. The potential genetic markers were developed and added into the physical map in silico. The gene features of these assembled sequences were analyzed using gene prediction programs (Genscan, Genescan+, Genemark.Hmm, Netgene2), the tRNA prediction program (tRNAscan-SE), and database searches. Further characterization toward transcription mapping was executed using a combination of the public rice expressed sequence tag (EST) database (75,000 ESTs downloaded from Genbank) screening and other database searches. Together, the physical and transcript maps described here serve as basic resources for further genome study.