Fagaceae Genomics Web

This project, entitled "Genomic Tool Development for the Fagaceae", intends to construct and integrate genetic and physical maps in the genus Castanea and develop comparative genomic resources for Northern red oak (Quercus rubra), White oak (Quercus alba), and American beech (Fagus grandifolia).

Primary support for this project comes from the Plant Genome Research Program number: NSF-PGRP 0605135 . Elements of this page were solely supported by CUGI . The American Chestnut Foundation has and does support genomic tool development in the Fagaceae.

The phases are listed below. Status updates are included with links to examine or download the data.

Mapping Populations

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.

cDNA Library Construction

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.

BAC Library Construction

Objective:
A 20 X coverage BAC library will be constructed using partial digestions with BstyI (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.

EST Sequencing

Objective:
Large scale EST sequencing has been carried out for Chinese chestnut, American chestnut, red oak, American white oak and American beech.
Status:
Extensive 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). Two more libraries are being sequenced now. Another 10K cDNA sequences have been completed on a Sanger sequencing platform.

Comparative Sequence Analysis

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, Populus proteins, Cryphonectria parasitica nucleotide sequences from GenBank, and the Swiss-Prot protein database. Candidate SSRs and SNPs have been generated from the contigs.

Marker Development and Verification

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:
Candidate SSRs and SNPs from the 454 sequence data have been identified. Over 300 have been screened with more coming soon.

Genetic Mapping

Objective:
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.

Breeding and Disease Screening

Objective:
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.

Physical Map Construction

Objective:
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. The second BAC library (EcoR1) has been fingerprinted and an FPC build is in progress. Updates to webFPC will occur as more of the physical map is developed and refined.

Integration of Genetic and Physical Maps

Objective:
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:
Overgos are currently being developed from the successful SSR and SNP markers.