Open Access Highly Accessed Research article

High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence

David L Hyten1*, Steven B Cannon2, Qijian Song13, Nathan Weeks2, Edward W Fickus1, Randy C Shoemaker2, James E Specht4, Andrew D Farmer5, Gregory D May5 and Perry B Cregan1

Author Affiliations

1 Soybean Genomics and Improvement Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA

2 Department of Agronomy, U.S. Department of Agriculture, Agricultural Research Service, Iowa State University, Ames, IA 50011, USA

3 Department Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA

4 Department of Agronomy and Horticulture, University of Nebraska Lincoln, Lincoln, Nebraska, NE 68583, USA

5 National Center for Genome Resources, Santa Fe, NM 87505, USA

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BMC Genomics 2010, 11:38  doi:10.1186/1471-2164-11-38

Published: 15 January 2010

Additional files

Additional file 1:

SoyOPA-4 SNPs. The 1,536 SNPs along with the flanking sequence to design the GoldenGate assay SoyOPA-4.

Format: XLS Size: 382KB Download file

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Additional file 2:

Williams 82 × PI 468916 genetic map. The high-resolution Williams 82 × PI 468916 genetic map created with 1,790 SNPs genotyped on 268 or 444 recombinant inbred lines (RILs). Also shown is the high-resolution map resulting when only using the 1,254 SNPs genotyped with SoyOPA-4 on 444 RILs and the Consensus Map 4.0 position for any SNPs in common between the two genetic maps.

Format: XLS Size: 312KB Download file

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Additional file 3:

Williams 82 × PI 468916 comparison to the soybean Consensus Map 4.0. The charts of the 20 linkage groups from the Consensus Map 4.0 (left chart) compared to the same 20 linkage groups produced from the 444 recombinant inbred lines of Williams 82 × PI 468916 (right chart).

Format: PPT Size: 1.1MB Download file

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