1a.Objectives (from AD-416):
To complete sequencing and assembly of the cranberry genome via bioinformatics, making the cranberry genome publically available and for joint ARS and Cooperator's research. Ultimately, assembly will inter alia assist in mapping, accession identification, marker-assisted selection, and gene discovery.
1b.Approach (from AD-416):
1. Generate a draft genome from the SOLiD sequence data already acquired. 2. Create a new genomic library from the same accession, using 500 and/or 250 kb inserts, for Illumina/Solexa sequencing to improve the draft assembly. 3. Assemble the genome using bioinformatics. 4. Identify gene markers in the cranberry genome through Simple Sequence Repeats (SSRs) in the genome and isolate genes of interest.
The SOLiD sequence data were assembled and used to generate SSR markers. This work was published (Georgi et al., 2012. Cranberry microsatellite marker development from assembled next-generation genomic sequence, Molec. Breeding 30:227-237). The new genomic libraries were created and sequenced on the Illumina platform. We designed and tested nearly 300 primer sets for amplification and tested for polymorphism across four populations of cranberry seedlings segregating for fruit rot resistance. Some markers were identified that mark QTL for fruit rot resistance. The first-generation map and some identified QTL were described in a publication (Georgi et al., 2013. The first genetic map of the American cranberry: exploration of synteny conservation and quantitative trait loci, Theor. Appl. Genet. 126:673-692).