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 chimeric contigs 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 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 3 rd 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/pro duct/8538-PPE-02203/ username: cacao password: ty8$q1a http://www.genome.clemson.edu/orders/pro duct/8538-PPE-02203/