Project Number: 1275-21000-263-23
Project Type: Reimbursable

Start Date: Jun 01, 2007
End Date: May 31, 2009

Objective:
The first objective of this research is to create a genetic mapping population via a cross of the soybean cultivar Williams 82 with the wild soybean (G. soja) parent PI 468916. The second objective is to create and sequence a plasmid library of PI 468916 DNA and compare the sequences of the plasmid clones with the draft whole genome sequence of Williams 82 that is being created by the Department of Energy, Joint Genome Institute (DOE, JGI). This will allow the discovery of single nucleotide sequence differences or SNPs between Williams 82 and the PI 468916. The third objective is the mapping of the SNP DNA markers in the Williams 82 x PI 468916 mapping population. The resulting mapping data will anchor sequence contigs of Williams 82 to the soybean genetic map and assist in the assembly of the Williams 82 whole genome sequence.

Approach:
A plasmid library of approximately 30,000 clones with an insert size of 2000 basepairs will be created using genomic DNA of PI 468916. Each clone will be sequenced from both ends using Sanger sequencing on the ABI3730. The resulting sequence data will be compared to the DOE, JGI draft sequence of Williams 82. This comparison will firstly eliminate sequences that are repetitive. Those sequences that align with sequence in Williams 82 contigs that are already anchored to the genetic map will be discarded. Sequence variants will be identified in the remaining PI 468916-Williams 82 alignments using Phred sequence quality scores. Only high quality variants (Phred score > 25) with a high probability of being real variants (SNPs), rather than sequencing errors, will be considered. In addition, SNPs that occur in fragments in which there are 100 basepairs of high quality sequence data on either side of the SNP will be selected for the development of SNP detection assays using the Illumina GoldenGate assay. SNPs will be genetically mapping on the Williams 82 x PI 468916 mapping population using the Illumina BeadStation 500.