Objective:
Establish new large mapping populations in Chinese and American chestnut.

Status:
A total of 476 C x C seed were established in pots in greenhouses at CAES. Seed represent 2 crosses: Mahogany x Nanking (304 seed) and Vanuxem x Nanking (172 seed). 135 seed from the F2 created at CAES were also planted.

Objective:
cDNA Libraries will be constructed for a suite of tissues, both infected and uninfected, from Chinese and American chestnuts, American beech, and both red and white oaks by K.M. Baier & W.A. Powell at SUNY-ESF.

Status: Completed.
Libraries for 5 species, 6 types of tissues, healthy and diseased trees have been completed and used for sequencing. A chart of libraries that were ultimately used for sequencing is here.

Objective:
A 20 X coverage BAC library will be constructed using partial digestions with Bsty1 (10X) and HindIII (10X). Our target is an average insert size of 100 kb for 160,000 BAC clones (200 384 well plates).

Status: Completed.
The libraries have been successfully completed. More statistics can be found here.

Objective: Large scale EST sequencing will be carried out for Chinese chestnut (Castanea mollissima), American chestnut, red oak (Quercus rubra), American white oak (Quercus alba) and American beech.

Status:
454 sequencing has been completed and data are being summarized/analysed for inclusion in two manuscripts currently under construction. Nearly 380 million bases were sequenced at an average read length of 230 bp yielding over 120K contigs, 21K of which were considered large (>700 bp).

The first 10K cDNA sequences have been completed. Completion of an additional 10K reads has been placed on hold while we evaluate our current results.

The currently available sequences can be found here.

Objective: EST sequences will be analyzed for homology and orthology, and then for diversity within and between species of the Fagaceae. Candidate SNPs and SSRs will be identified. Unigenes/transcript contigs will be classified for putative functions according to GO ontology.

Status:
The available sequences have been compared to Arabidopsis proteins and Populus proteins as well as Cryphonectria parasitica nucleotide sequences from GenBank.

Objective: Establish new large mapping populations in Chinese and American Chestnut. Using candidates derived from sequence data, develop SNPS and SSRs to distinguish Chinese and American genome segments. Identify 200 markers that distinguish Chinese and American chromosome segments.

Status: A pipeline has been defined for developing markers for genetic mapping and joining genetic and physical maps.. A DNA panel (12 trees: 2 Chinese Chestnut, 2 American Chestnut, 2 European Chestnut, 2 Red Oak, 2 American Beech, and 2 European white oak parents) will be used for screening for polymorphisms. We are awaiting European samples, which are expected to arrive by mid-June 07. 140 SSR markers dev eloped by EU collaborators (EvolTree Project) have been made available for testing against our CC and AC parents (to begin mid-June 07). Over 500 potential simple sequence repeats in ESTs were identified in the first GS 20/454 sequencing runs. We will prioritize potential markers for screening beginning with SSRs and SNPs that show polymorphism.
When more information and data are released, they can be accessed here.

Carry out mapping and screening using chestnut SNPs and SSRs. Establish basis for segregation distortion in the AC x CC F2 mapping population. Resolve the basis of the missing linkage group in the AC x CC linkage map. Develop marker association genetic screening for BC3 and BC4 progeny.

Status: This part of the project will begin when SNP and SSR marker development is completed. Seeds from previous crosses have been collected, vernalized and planted in greenhouses to create the mapping population in preparation for this phase.
When maps and information are released, they can be accessed here.

Establish new F2 populations from an F1 x F1 cross to confirm the extent of dominance for resistance QTLs. Locate Chinese chromosome segments in backcross progeny. Association of markers with resistance will be confirmed in the greater BC3 and BC4 populations by trait association analysis statistics.

Status:
Resistance screening is slated to begin in the second quarter of 2009 after marker development is completed.

Select BACs by overgo hybridization screening with EST probes. Carry out BAC fingerprinting and BAC end sequencing.

Status: The BstyI 10X coverage BAC library fingerprinting was completed and an initial contig build is available. To date, 8K clones of the second BAC library (EcoR1) have been fingerprinted. Updates to webFPC will occur on a regular basis as more of the physical map is developed and refined.

Physical mapping results can be viewed here.

Develop an integrated genetic and physical map of Chinese chestnut. Identify BAC contigs in regions of the major QTLs for resistance to C. parasitica for post-project sequencing to be proposed to JGI.

Status:
This is slated to begin in the third quarter of 2008. Results will be made available here.