Fluorescence in situ hybridization (FISH)-based karyotype of Theobroma cacao Matina 1-6. A FISH cocktail comprised of two Cent-Tc oligonucleotide probes plus four BAC clones permitted identification of the ten chromosome pairs. (A) Ideogram of the T. cacao Matina 1-6 karyotype. Centromeres are coded in accordance with the color and size of the combined FISH signals for OLI-07 (green pseudo-colored) and OLI-13 (red pseudo-colored). Bacterial artificial chromosome (BAC) probes (red or green) are indicated by paired dots near chromosome termini. The following BACs were used for probes: for Tc03, TcC_Ba057I03 and TcC_Ba027M06; for Tc04, TcC_BB065A03; for Tc06, TcC_Ba018I22. Relative chromosome sizes are not indicated, with the exception of the satellite arm of Tc07, which is shown as a knob. (B) Chromosomes labeled with the FISH cocktail arranged by chromosome number. Chromosomes are discriminated as follows: Tc01 has the second-brightest yellow centromere. Tc02 has the brightest yellow centromere. Tc03, Tc04, Tc06, and Tc07 all have similar centromere labeling (pure green), but are differentiated based on unique BAC probe labeling: Tc03 is labeled at each end by green BAC probes; Tc04 is labeled at one end by a green BAC probe; Tc06 is labeled at one end by a red BAC probe; and Tc09 is not labeled by BAC probes. Tc05 has the second-brightest red centromere; Tc08 has the brightest red centromere with an 'internal' green domain; and Tc09 has the brightest yellow-green centromere and is much longer than Tc10, which has the second-brightest yellow-green centromere. (C) DAPI channel image of chromosomes in (B). The satellite arms of Tc07 are above the centromeres. (D) A FISH image containing a complete chromosome spread. (E) Corresponding DAPI channel image from which chromosomes in (C) were extracted.