Fig. S1 Detected somatic genetic variation in linkage group 1.

Fig. S2 Visualization of the relative efficiency of enzymes MroI and BseAI in cutting methylated or unmethylated templates as revealed by real-time quantitative PCR (RT-qPCR).

Fig. S3 Effect of primary and secondary embryogenesis on the appearance of staminode I products in the LCT EEN 162/S-1010 regenerant population.

Table S1 Single sequence repeat (SSR) allele sizes for cocoa genotypes.

Table S2 Sequences (5′–3′) of primers used for microsatellite and methylation-sensitive amplified polymorphism (MSAP) analysis.

Table S3 Summary of the number of fragments displaying each class of epigenetic polymorphism between floral and leaf tissues in Theobroma cacao.

Methods S1 Experimental procedure to quantify differential sensitivity of MroI and BseAI to cytosine methylation.

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