Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Poster: Genome Sequencing & ESTs
            

THE SOYBEAN INTEGRATED PHYSICAL AND GENETIC MAP: PROGRESS TOWARD FUNCTIONAL, HIGH DENSITY GENE MAPS

¹ Department of Plant Soil and General Agriculture, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415 USA

² Department of Soil and Crop Sciences, Crop Biotechnology Center, Texas A & M University, College Station, TX 77843-2123 USA

A marker anchored physical map derived from bacterial artificial chromosomes (BACs) was constructed. We used 476 SSR primer pairs to identify 1,404 positive clones, an average of 2.95 clones per primer (Fig. 1). Of these 370 markers have anchored 930 individual BACs after eliminating false positives and paralogs by fingerprinting. The genetic map location for all markers and plate addresses for all clones can be viewed at http://www.coalab.siu.edu/genome/. The data indicate the library represents 3 fold genome coverage compared to the 4.5 fold predicted. The map appeared to contain 96.7% of the markers tested Fingerprinting and SNP marker integration showed that about 10% of the satellite anchored BACs derived from homeologous loci detected with the microsatellite primers that are not strictly allele specific. A further 150 satellites are in the process of being integrated. We have fingerprinted 90,624 BACs and BIBACs to date. There are 38,400 clones from the HindIII BIBAC library, 21,504 clones from the BamHI BIBAC library and 30,720 clones from the new EcoRI BAC library. Fingerprinting BACs that anchor the local physical maps of soybean c.v Williams has incorporated about additional microsatellite markers and RFLP markers. BAC fingerprints were used to create an FPC database for investigator driven contig assembly (see http://hbz.tamu.edu/ - Physical Mapping/Soy Map). Contigs representing the soybean physical map have been assembled and posted. We will use the database to build minimally overlapping clone tiles for high-throughput gene (EST) mapping, large-scale genome sequencing and targeted DNA marker development in phase 2 of this project. This work was supported by NSF project #9872635.