FPC Contig Maps

View Wheat Contig Maps by Using FPC Web Viewer

View Wheat Contig Maps by Searching WheatDB

Wheat FPC database will be available soon to be downloaded for viewing using FPC software

Five new genomic DNA libraries of Ae. tauschii ssp. strangulata from Armenia (line AL8/78-2-2) were constructed in a BAC vector and a plant-transformation-competent BIBAC vector utilizing three different restriction sites (EcoRI, BamHI, and HindIII). An automated fingerprinting procedure using capillary DNA sequencers are being used to fingerprint the BAC and BIBAC clones and determine their DNA fragment size. BAC/BIBAC contigs are being assembled weekly.

The libraries are completed and range in size from 54,224 to 76,800 clones with an average insert sizes from 149 to 190 kb (See Progress page). A total of 255,744 clones (~11-fold genome coverage) are selected and have being fingerprinted (see following table) and DNA fragments will be sized by ABI 3100 capillary electrophoresis DNA sequencers (see Physical Mapping with BACs page).  

Of the 255,744 BACs and BIBACs to be fingerprinted, 110,592 clones (below table) have been arrayed onto six high-density membranes and probed with pools of EST and RFLP clones. An insert-pooling technique are used to maximize efficiency of hybridization. More than 60,000 wheat ESTs are available, ~23,000 unique wheat genes have been identified, and 1,230 EST singletons have been mapped to wheat deletion bins by the effort of the Wheat EST Genomic Project (NSF DBI-9975989). Over 1,000 RFLP markers have been mapped genetically and about half of them mapped into deletion lines. Thus, anchoring the EST and RFLP clones to BAC contigs will integrate the contigs into the wheat deletion map.

Selection of Ae. tauschii BACs and BIBACs to be analyzed for physical mapping
Library Code Library/Vector Average Insert Size (kb) Clones Being Fingerprinted Clones Being Screened
Plates No. Coverage Plates No. Coverage
061-WHD-RI EcoRI/pECBAC1 167 1 - 142 54,528 2.2X 1 - 5, 11 - 53 18,432 0.8 X
062-WHD-BI BamHI/pECBAC1 149 1 - 156 59,904 2.2X 1 - 16, 49 - 96 24,576 1.0 X
063-WHD-BI BamHI/pCLD04541 174 1 - 80 30,720 1.4X 1 - 48 18,432 0.8 X
064-WHD-H3 HindIII/pECBAC1 189 1 - 156 59,904 2.8X 1 - 32, 49 - 96 30,720 1.4 X
065-WHD-H3 HindIII/pCLD04541 190 1 - 132 50,688 2.2X 1 - 48 18,432 0.8 X
Total   524  255,744 10.8X  288  110,592  4.8 X

Contig Assembly:

FPC v6.0 is used to assembly contigs. The tolerance and cutoff are 0.5 bps and 1e-30, seperately. Right now no any manual editing is done for contigs.

Current Status of Wheat D Genome Contigs:

Date Clone Marker Anchored Marker Contig Singleton Total Bands
05/09/02 3025 4 0 176 2335 302176
06/25/02 15484 109 0 818 13608 1613732

Clone Naming:

Clones starting with a "RI" are from the EcoRI/pECBAC1 library (061-WHD-RI).
Clones starting with a "HI" are from the BamHI/pECBAC1 library (062-WHD-BI).
Clones starting with a "BB" are from the BamHI/pCLD04541 library (063-WHD-BI).
Clones starting with a "HD" are from the HindIII/pECBAC1(064-WHD-H3).
Clones starting with a "HB" are from the HindIII/pCLD04541 (065-WHD-H3).

Viewing FPC maps of other research projects:

Last modified on June 25, 2002
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