Running Title: A Physical Map of the Soybean Genome

ABSTRACT- 2-Wu et al. We report a genome-wide, bacterial artificial chromosome (BAC) and planttransformation-competent binary large-insert plasmid clone (hereafter BIBAC)based physical map of the soybean genome. The map was constructed from 78,001 clones from five soybean BAC and BIBAC libraries representing 9.6 haploid genomes and three cultivars. The map consisted of 2,905 BAC/BIBAC contigs, and was estimated to span 1,408 Mb in physical length. The physical length is about 293 Mb greater than the expected 1,115-Mb genome size of the species, indicating that most, if not all, of the contigs remain overlapped. We evaluated the reliability of the map contigs using different contig assembly strategies, independent contig building methods, DNA marker screening results of the BACs and BIBACs and different fingerprinting methods, and the results showed that the map was assembled properly. Furthermore, we have integrated 781 of the contigs spanning 663 Mbp (59.5%) of the soybean genome into the existing soybean composite genetic map using 273 SSR and 115 RFLP markers. This map represents the first genome-wide, BAC/BIBAC-based physical map of soybean and will provide a powerful platform for many areas of soybean genome research, including large-scale genome sequencing, target marker development, gene mapping, and gene and quantitative trait locus (QTL) cloning. The inclusion of BIBACs in the map will further streamline the utility of the map for positional cloning of genes and QTLs, and functional analysis of soybean genomic sequences. [The supplemental material on the clone fingerprint database and contigs of the physical map is available online a