Theobroma cacao Integrated Physical and Genetic Map

2 BAC Libraries250 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.

• FpMiner – Assess quality of sizing and remove vector/repeat fragments/poor quality• Contain 20-250 bands

Percentage of Bands per Clone

<60 <80 <100 <120 <140 <1600

5

10

15

20

25

30

Percentage of Bands

N = 123 bands per clone

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

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)

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

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

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

Access to Data

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