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Title: High-Throughput SNP Discovery through Deep Resequencing of a Reduced Representation Library to Anchor and Orient Scaffolds in the Soybean Whole Genome Sequence

item Hyten, David
item Cannon, Steven
item SONG, QIJIAN - University Of Maryland
item Weeks, Nathan
item Fickus, Edward
item Shoemaker, Randy
item SPECHT, JAMES - University Of Nebraska
item MAY, GREG - National Center For Genome Resources
item Cregan, Perry

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/30/2009
Publication Date: 1/1/2010
Citation: Hyten, D.L., Cannon, S.B., Song, Q., Weeks, N.T., Fickus, E.W., Shoemaker, R.C., Specht, J.E., May, G.D., Cregan, P.B. 2010. High-Throughput SNP Discovery through Deep Resequencing of a Reduced Representation Library to Anchor and Orient Scaffolds in the Soybean Whole Genome Sequence. Biomed Central (BMC) Genomics. 11:38.

Interpretive Summary: Molecular markers have become extremely important in helping to improve crops such as soybean through gene discovery. However, the number of single nucleotide polymorphisms (SNPs) available for the soybean genome needs to be increased to help map genes that contribute to agronomically important traits quickly and cost effectively. A new method of SNP discovery has been applied to soybean which uses new DNA sequencing techniques has been used to find a total of 20,119 SNPs. A total of 1,240 of these SNP markers were used to help assemble the soybean genome sequence produced by the Department of Energy, Joint Genome institute. The large number of new markers discovered and mapped will be used by crop researchers, crop breeders and seed companies to increase the efficiency of molecular marker application in soybean for gene discovery and genetic improvement.

Technical Abstract: 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 only properly oriented 66% of the sequence scaffolds. To find additional single nucleotide polymorphism (SNP) markers for additional anchoring and orienting of the genome sequence we combined next generation sequencing and high-throughput genotyping to obtain a high resolution genetic map that could be used to anchor and orient most of the remaining genome and help validate the integrity of the scaffold builds. A total of 20,119 predicted SNPs were discovered using a reduced representation library 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 which 1,240 markers were targeted to unachored or unoriented sequence scaffolds, thereby increasing the amount of anchored sequence to 97%. We have demonstrated how next generation sequencing combined with high-throughput SNP detection assays can quickly discover large numbers of SNPs which can be used to create a high resolution genetic map to assist in the assembly of scaffolds from whole genome shotgun sequences into pseudomolecules which represent the chromosomes of the organism.