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Toward a Reference Sequence of the Soybean Genome: A Multiagency Effort

S.A. Jackson, Dep. of Agronomy, Purdue Univ., 915 W. State St., West Lafayette, IN 47906; D. Rokhsar, JGI Production Genomics Facility, 2800 Mitchell Dr., Walnut Creek, CA 94598; G. Stacey, National Center for Soybean Biotechnology, Div. of Plant Sci. and Biochemistry, Dep. of Molecular Microbiology and Immunology, Univ. of Missouri, Columbia, MO 65211; R.C. Shoemaker, Corn Insect and Crop Genetics Research Unit, Ames, IA 50011; J. Schmutz and J. Grimwood, Stanford Human Genome Center, Dep. of Genetics, Stanford Univ. School of Medicine, 975 California Ave., Palo Alto, CA 94304

View larger version (28K): [in this window] [in a new window]   Fig. 1. cMap view of bacterial artificial chromosome (BAC) contigs integrated with genetic map with QTL. From right to left, light bars are QTL, LG_A1 equals section of linkage group A1, solid bar connected by thin lines to green loci is WmContig3588, green loci are genetic markers that anchor this contig, and green and black bars are BACs (green means has one or more overgo or genetic marker associated, black means none). Circles next to each BAC name indicate which and what kind of marker identify that BAC (No. of BACs hit referenced by OG1, only 2 hit OG2, or OG3).

View larger version (20K): [in this window] [in a new window]   Fig. 2. Schematic of genome mapping, genetic and physical, and integration of whole-genome shotgun sequences (WGSS). A typical chromosome (ideogram) is shown at left of figure, immediately to the right is a linkage map with units of centimorgans. Genetic markers on the linkage map with sequence information can be used to anchor bacterial artificial chromosomes (BACs) or BAC contigs to the genetic map (integrated map). Individual BACs (third layer from right) are assembled into contigs based on fingerprint information (FPC map). Traditionally, overlapping BACs are used to make a BAC tiling path for sequencing (i.e., yellow BAC clones). End sequences from BACs (BES, orange balls on end of BACs) are used to provide large spanning clones for assembling WGSS and, in the interim, to provide genetic markers to further anchor BAC contigs. A WGSS is made in the form of end-sequenced randomly sheared clones of various sizes (colored bars at right of figure). Paired sequences are computationally assembled into contigs (completely overlapping sequence information) and then scaffolds (ordered contigs where clones span sequence gaps). The BES and sequence-based markers are used to anchor sequence contigs and scaffolds to the BAC-based physical and genetic maps.