Hyten et al. BMC Genomics 2010, 11:38 http://www.biomedcentral.com/1471-2164/11/38 R E S E A R C H A R T I C L E Open Access 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 Song1,3, Nathan Weeks2, Edward W Fickus1, Randy C Shoemaker2, James E Specht4, Andrew D Farmer5, Gregory D May5, Perry B Cregan1 Abstract Background: The Soybean Consensus Map 4.0 facilitated the anchoring of 95.6% of the soybean whole genome sequence developed by the Joint Genome Institute, Department of Energy, but its marker density was only sufficient to properly orient 66% of the sequence scaffolds. The discovery and genetic mapping of more single nucleotide polymorphism (SNP) markers were needed to anchor and orient the remaining genome sequence. To that end, next generation sequencing and high-throughput genotyping were combined to obtain a much higher resolution genetic map that could be used to anchor and orient most of the remaining sequence and to help validate the integrity of the existing scaffold builds. Results: A total of 7,108 to 25,047 predicted SNPs were discovered using a reduced representation library that was subsequently sequenced by the Illumina sequence-by-synthesis method on the clonal single molecule array platform. Using multiple SNP prediction methods, the validation rate of these SNPs ranged from 79% to 92.5%. A high resolution genetic map using 444 recombinant inbred lines was created with 1,790 SNP markers. Of the 1,790 mapped SNP markers, 1,240 markers had been selectively chosen to target existing unanchored or un-oriented sequence scaffolds, thereby increasing the amount of anchored sequence to 97%. Conclusion: We have demonstrated how next generation sequencing was combined with high-throughput SNP detection assays to quickly discover large numbers of SNPs. Those SNPs were then used to create a high resolution genetic map that assisted in the assembly of scaffolds from the 8× whole genome shotgun sequences into pseudomolecules corresponding to chromosomes of the organism. Background The Department of Energy, Joint Genome Institute (JGI) has completed an 8× shotgun draft sequence of the soy- bean cultivar Williams 82 [1]. For initial assembly of the genome sequence, a preliminary 4× and 6.5× scaffold assembly was produced by the JGI, with the 6.5× assem- bly released to the public http://www.phytozome.net. This 6.5× assembly contained a total of 3,118 scaffolds totaling 993.5 Mb of sequence. Using the soybean Con- sensus Map 4.0, which contains a total of 5,500 markers * Correspondence: david.hyten@ars.usda.gov 1Soybean Genomics and Improvement Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA [2], Schmutz et al., [1] associated a total of 296 of the 6.5× scaffolds with the genetic map. These scaffolds consisted of 949 Mb, or 95.6% of the total 6.5× assembly. The initial assembly resulted in the anchoring of a large proportion of the genome to create 20 psuedomo- lecules corresponding with the 20 soybean chromo- somes. However, it was subsequently evident that this initial psuedomolecule build had a significant number of assembly problems [1]. First and foremost was the insuf- ficient resolution afforded by the Consensus Map 4.0, which had been constructed using five separate mapping populations and with most of the markers mapped in less than 100 individuals [2]. Second, many of the © 2010 Hyten et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.