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Theobroma cacao Integrated Physical and Genetic Map

Theobroma cacao Integrated Physical and Genetic Map. 2 BAC Libraries 250 Genetic Markers. Quality Statistics (Both BAC Libs ). Number of BACs Fingerprinted: 72,192 Number of BACs pass Q/C: 67,408 (93.3%) Criteria: GeneMapper - Sizing of fragments in comparison so size std.

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Theobroma cacao Integrated Physical and Genetic Map

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  1. Theobroma cacao Integrated Physical and Genetic Map 2 BAC Libraries 250 Genetic Markers

  2. Quality Statistics (Both BAC Libs) • Number of BACs Fingerprinted: 72,192 • Number of BACs pass Q/C: 67,408 (93.3%) • Criteria: • GeneMapper - Sizing of fragments in comparison so size std. • FpMiner – Assess quality of sizing and remove vector/repeat fragments/poor quality • Contain 20-250 bands

  3. Percentage of Bands per Clone N = 123 bands per clone

  4. Fingerprint Assembly Parameters • 1e-70 ; Tolerance of 3 • Means: User supplied cutoff on the Sulston score that FPC uses to determine if two clones overlap • DQer: Build was subject to DQer • Detects possible chimericcontigs and breaks them apart • Ends Ends: build was subject to Ends Ends function • Detects possible contigs to merge

  5. Physical Assembly (FPC) • Number of BACs incorporated incontigs: 62,830 (87%) • Number of Contigs: 610 • Estimated Genome Coverage: 19X fingerprint coverage • (480Mbp genome size) • Longest Contig: 5.03 Mbp (Estimated)

  6. Comparison to a Recently Published Map (similar experimental design) • Brassicarapa: • 22.5X BAC library coverage • 114 bands/clone • 1e-45 and included only 70% of the clones • 1e-70 included only 40% of the clones • 1,417 contigs; 1.3X total fingerprint coverage

  7. Genetic Marker Data • Total markers hybridized: 250 • Success rate: 220/250 (88%) • Link to Markers associated with contigs • 250_markers_contigs_v2.xlsx • Contig 1179 Contains chloroplast DNA, other possible chloroplast contigs are 1630,1552,1444 and 1454

  8. Integration and Lab Update • After 3rd BAC fingerprints are added: • Final manual analysis of contigs • Merging • Breaking • Consider all genetic data points and BAC-end sequence • Lab Update: Finish by end of July

  9. Access to Data • http://www.genome.clemson.edu/orders/product/8538-PPE-02203/username: cacaopassword: ty8$q1a

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