Download
theobroma cacao integrated physical and genetic map n.
Skip this Video
Loading SlideShow in 5 Seconds..
Theobroma cacao Integrated Physical and Genetic Map PowerPoint Presentation
Download Presentation
Theobroma cacao Integrated Physical and Genetic Map

Theobroma cacao Integrated Physical and Genetic Map

100 Vues Download Presentation
Télécharger la présentation

Theobroma cacao Integrated Physical and Genetic Map

- - - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript

  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