2005 Annual Report 4d.Progress report. This report serves to document research conducted under a Specific Cooperative Agreement between ARS and Texas A&M University. Additional details of this research can be found in the report of the parent project 1907-21000-014-00D Comparative Plant Genomics. This work focuses on increasing our understanding of the sorghum genome organization and QTL associated with crop enhancement. In the past year the major focus of research has been mapping gene sequences based on ESTs and GSS reads from sorghum to the sorghum genome, refining the tiling path of sorghum chromosome 3 and comparative analysis with rice. Seventy eight primers sets were developed to SSRs found in sorghum sequences and tested in the sorghum mapping populations. Of these 47 primers were polymorphic indicating these were suitable for genetic mapping. In conjunction with an NSF funded plant genome project, 612 EST-STS sequences were used to screen six-dimension BAC pools and HICF fingerprinting was used to improve the TAMU physical map. Of the primer pairs 466 amplified, identifying 2000 sorghum BACs that were fingerprinted. Integration of the data sets has led to the construction of a high quality map of sorghum 3 that contains, 39 contigs covering a total size of ~ 61 MB.