|12-425 Project Manager: D. C. Jones|
GENOME RESEQUENCING OF SELECT COTTON DIPLOID ACCESSIONS
Allen Van Deynze, University of California, Davis
We re-sequenced 4 A-genome diploid accessions and 5 D-genome diploid accessions. Our plan was to have 5 genomes of each. One of the samples (A1-73) had DNA quality issues and the sequence that was generated was a failure. We have created a new library and re-sequenced it on other funds. The 50bp SE data are currently being processed this week (Jan 23rd 2013). Plans are to generate more sequence from this library of a 100bp PE.
The current mapping results of reads continues. All of these reads have been mapped to the D-genome of cotton using our new tool called PolyCat. This tool has recently been accepted for publication in G3:Genes|Genetics|Genomes. Using this tool we are able to normalize GSNAP mapping efficiency of A-reads to the D-genome. There are still improvements to be made, but we are pleased with the progress.
We have identified approximately 26M robust SNPs between the A- and D- diploid genomes. Any hirsutum SNP-assay should be screened against this set of homoeo-SNPs prior to buying primers - because you wouldn't want to target a SNP between genomes with an assay intended for alleles. We are diligently working on the data analysis and need a few more weeks to be more confident in our homoeo- and allele-SNP calls. We anticipate publishing a paper containing our findings this year. We are also uploading the data to the NCBI Sequence Read Archive for public consumption, though the data access will not be released until we have a better assessment on the results.
|Project Year: 2012|
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