2005 Annual Report 4d.Progress report. This report serves to document research conducted under a Specific Cooperative Agreement between ARS and Cold Spring Harbor Laboratory. 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 extending resources and continuing to develop new resources to increase our understanding of complex genome organization of cereals and develop methods to sequence large plant genomes. Work over the past year has yielded sequences from sorghum and maize genomes for the purpose of generating sequence data sets that are from syntenic regions in rice, which will improve the understanding of gene movement and develop methods to allow complex cereal genomes to better leverage the nearly complete rice genome. In the past year, the McCombie group has generated five finished BAC sequences from Maize chromosome 8 (542,582 bp), and two libraries made from a total of 70 maize BACs (9,731,098), and 14 libraries from a 56 sorghum BACs for sequence skimming (11,219,944 bp. The regions sequenced are from sorghum chromosome 3 and maize chromosome 8, which are syntenic with rice chromosome 1 between the 35 and 40 Mb. A major QTL for aluminum tolerance is found in both rice and sorghum in these regions. The data generated from this project will help to better annotate the rice genome sequence, develop minimum sequencing strategies to capture genes from cereal crops base on synteny, better understand gene movement, and accelerate the identification of genes involved in aluminum tolerance.