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Figure 1. The genomic linkage map for the ‘Pound 7’ x ‘UF 273’ F1 cacao population, the position of each marker on each chromosome, and charts showing the LOD curve for each trait, with significant quantitative trait loci (QTLs) and location on each respective LG. The peak of the LOD curve lies within the area denoted by the horizontal line in the thicker bar of the two bars (thick and thin) of the QTL confidence interval, corresponding to 1-LOD and 2-LOD intervals in each direction. QTLs are labeled as follows: FrosPod_EXT1, FrosPod_INT1; frosty pod external resistance 1, frosty pod internal resistance 1, and similarly for those ending in 2 and 3. Phytoph1; black pod resistance1, and similarly for those ending in 2 and 3. Jor1; First QTL for centimorgan to formation of first jorquette, and similarly for second QTL for formation of first jorquette. Pod Color1 is the first QTL for pod color; Ave_gr_rt1 is the first QTL for average growth rate of trunk diameter. Each linkage group is marked with the number from the reference map (LG 1, etc.). Pod color has no corresponding curve, being a categorical variable and based on a chi-squared statistic, instead of a LOD score.
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