We are developing a sequence-ready, integrated physical and genetic map of chromosome 3A (~802 Mb) of wheat. Chromosome-arm specific BAC libraries of the 3A short (3AS, 110,692 BACs with 25x coverage), and 3A long arms (3AL, 78,952 BACs with 15x coverage) were developed and fingerprinted. We assembled 97,144 BAC clones into 1,104 contigs with an average length of 662 kb and an average of 81 clones/contig, covering over 90% of 3AS and 87% of 3AL. The MTPs of ~5,300 BAC clones from 3AS and ~5,300 from 3AL have been identified for sequencing. EST-STS and BES-based markers were developed to anchor the fingerprint map, and ~500 ESTs, ~500 ISBPs, and ~500 SSRs were anchored on the BAC contigs using six-dimensional BAC pools or BAC-end sequencing. To further improve the marker density, three-dimensional pools were developed from 2,743 BAC clones spaced along the MTP. We pooled 2,743 BACs in three dimensions and sequenced with ~6x coverage by 454 sequencing. The sequence was assembled into ~194,000 contigs and masked to identify gene-coding regions. Approximately 55% of the 194,000 contigs and over 70% of the gene-containing contigs were traced back to individual BAC clones. Nearly 2,900 genes were amplified and sequenced from the parents of the mapping population T. monococcum subsp. aegilopoides and subsp. monococcum, and SNPs have been identified. A high-throughput GoldenGateTM genotyping assay with 1,536 SNPs is being developed, and 480 recombinant inbred lines will be used to develop an integrated genetic and physical map of chromosome 3A of wheat.