Fermented cocoa from 100 individual trees (genotypes) representing 9 cacao Genotype Groups. Relative amounts of chemical compounds and scores of sensory attributes.

<p>Two-harvest averages by Genotype Group (GG) are indicated in the top part. GGs coded by colors according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054079#pone.0054079-Trognitz2" target="_blank">[3]</a> (B; blue, Y; yellow, O; orange, E; gray, G; green, S; steel gray, A; aqua, P; purple, R; red).</p><p>Bottom part of table; individual GGs are ranked for each character (in descending order from positive to negative contribution to high quality cocoa). The probability P (*; <0.05, **; <0.01, ***; <0.001) of a character as under control by the GG is indicated in the last line. To decide which GG represents the greatest potential (as a decision support in selection) one could consider those that occur most frequently among the (highlighted in bold-face) top three ranks. These would be GGs S and R, both occur 5 times.</p

Empirically determined mean values (expressed as percent of air-dried cocoa matter) and their statistics, generated and used at CIRAD to predict the quantity of several biochemical compounds in cocoa samples via Near Infrared Spectroscopy (NIRS).

<p>n; number of replicate measurements, Mean; arithmetic mean of all n measurements, SD; standard deviation, SE; standard error, R; coefficient of determination, SECV; standard error of cross validation.</p

Method of fermenting several small cocoa bean samples from individual trees under identical conditions of recommended traditional processing practice (“microfermentation technique”).

<p>A wooden fermentation box of 0.6×0.6×0.6-m dimensions is filled with a uniform 180-l batch of fresh beans. Up to eight meshes containing the individual samples are evenly distributed across two layers and perfectly embedded in the batch beans. Banana leaf is added as a cover and to provide optimal conditions for fermenting bacteria. The entire volume is rearranged manually every second day. Fermentation time uniformly was six days.</p

Summary of analyses of variance, average total quantities of chemical compounds, and sensory quality scores of cocoa samples.

<p>A quality attribute was considered as a function of Genotype Group (GG), Harvest, GG-Harvest interaction, and Trees (as replicates within a GG). The level of significance of variance components (F-test) is indicated (***; P<0.001, **; P<0.01, *; P<0.05, n.s.; not significant). There were 9 Genotype Groups (GG) and 95 (in harvest 1, non-fermented and fermented), 87 (harvest 2, non-fermented), and 78 (fermented) samples from individual trees. Df; error degrees of freedom (in analysis of variance). Grand mean quantities of compounds and their minima and maxima are presented in percent of dry matter.</p

Bar plots of the 15-SSR-genotype of 106 cacao trees from farms at Waslala that were used for assessment of cocoa quality and yield potential.

<p>A single bar represents a tree’s cumulative genotype consisting of fractions of ancestral genotype spectra. The in total nine genotype spectra were determined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054079#pone.0054079-Trognitz2" target="_blank">[3]</a> via Bayesian inference of population structure. Color coding of individual genotype spectra according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054079#pone.0054079-Trognitz2" target="_blank">[3]</a>. S; steel gray, G; green, P; purple, O; orange, R; red, E; gray, A; aqua, B; blue, Y; yellow. Their most probable ancestors and traditional cocoa types include for S; lower Amazon Forastero, G, P, O, and R; upper Amazon Forastero, E; upper Amazon Forastero isolated in coastal Ecuador, A, B; Trinitario, and Y; Criollo from Mesoamerica. The trees were grouped by their dominating genotype spectra. Group names of genotypes are indicated prior to tree name (as an example, tree W358 belongs to the S genotype group).</p

Plots of theobromine/caffeine (T/C) ratio (ordinate) vs. total caffeine content (abscissa) determined for samples of non-fermented cocoa.

<p>a; first harvest period 2008–9, b; second harvest (2009–11), c; two-harvest average.</p

Pairwise correlations of analytical (F; fermented and N; non-fermented samples) and sensory data of fermented samples obtained on up to 172 individual observations collected over two harvests of cocoa from 100 trees of smallholder farms around Waslala, Nicaragua.

<p>Color and shading intensity indicate levels of significance of correlations. Theobromine/caffeine (T/C) ratio and theobromine and fat contents of fermented cocoa (highlighted by green background) were the most important characteristics as determined in the analytics (see text).</p

Potential cocoa yield (<8% water content) of nine Genotype Groups (GG) and their ranking and differentiation by comparison of multiple means (t-test).

1<p>GG; Genotype Group, compare <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0054079#pone-0054079-g003" target="_blank">Figure 3</a>, Samplings; Number of observations made on the trees. The objective of 2 samplings per tree was not achieved for all trees. # Trees; Number of trees within a GG, Yield; Least-squares mean potential yield per tree (in kg). The potential maximum single-tree yield was estimated as (no fruits past cherelle wilt stage) * (no beans/fruit) * (bean weight). Bean weight was averaged on 100 dry (<8% water content) beans. t-Test; least significant difference of yield by GG determined by multiple t-Tests. Values with identical letters are not significantly different.</p

Allelic richness corrected for sample size by using rarefaction.

<p>This map shows the average number of alleles per locus in the 10-minutes grid cells applying a one-degree circular neighborhood and a correction by rarefaction to a minimum sample size of 20 trees.</p

Number of trees per grid after re-sampling.

<p>This map is made with a 10-minutes grid applying a one-degree circular neighborhood.</p