Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at .

No abstract

Cocoa black pod rot, a disease caused by Stramenopiles of the genus Phytophthora, and particularly by the pan-tropical species P. palmivora, causes serious production losses worldwide. In order to reduce the impact of these pests and diseases, preference is given to genetic control using resistant varieties and, to that end, breeders seek sources of resistance in wild cocoa trees. For instance, surveys of spontaneous cocoa trees in French Guiana between 1985 and 1995 led to the collection of abundant plant material forming a particular genetic group (the “Guiana” group). Following numerous one-off studies demonstrating the merits of this group as a source of resistance to Phytophthora, this article presents the results of a comprehensive study assessing the resistance of 186 “Guiana” clones in relation to the Guianan strain (GY 27) of P. palmivora. This study, undertaken in French Guiana, using an efficient methodology (ten series of tests and a statistical test adapted to the ordinal nature of the data) confirmed that the “Guiana” genetic group does indeed constitute an important source of resistance to P. palmivora, though with some variations depending on the demes of origin. Numerous clones (59) proved to be as resistant as the SCAVINA 6 resistance control, whilst nine were statistically more resistant. The “Resistant” and “Moderately Resistant” Guianan clones totalled 108 (58% of the total tested). Some of the clones more resistant than SCAVINA 6 could be incorporated into numerous cocoa breeding programmes, particularly those that also display other notable qualities. The same applies for numerous other clones equivalent to SCAVINA 6, especially the “elite”’ clones GU 134-B, GU 139-A and GU 285-A.

The detached pod test by spray method (DPT-SM) was developed to facilitate the screening of cacao genotypes for resistance to Phytophthora pod rot (PPR) caused by Phytophthora palmivora. The test has been adopted in many cacao research institutes, and it is imperative that its validity be assessed. In this study, 40 genotypes from various cacao groups were selected and screened for resistance to PPR by DPT-SM and field observations. Significant variation was observed in the reactions of the selected accessions based on the disease rating scale for DPT-SM and the percentage pod rot from field observations. A correlation coefficient of 0.68 (P<0.001) was observed between the results of year-1 and year-2 field observations. However, relatively lower correlation values were obtained between year-3 and year-1 (r=0.32; P=0.041) and year-3 and year-2 (r=0.35; P=0.025) field observations. A higher level of susceptibility was observed in the third year of field observations (63%) than in the first (15%) and second (25%) years. This suggests that the predisposing factors for PPR were unstable between the years of field observations. Data obtained from the Trinidad and Tobago Meteorological Services showed that the rainfall in November of the third year was higher than the amounts of rainfall in November of the first 2 years of field observations. This month marks the beginning of the main pod harvest season (November-February) and the high rainfall in November of the third year, and the presence of large number of mature pods may account in part for the increase in PPR in the third year of field observations than in the first 2 years. This shows that absolute reliance could not be placed on a single year of field observations in determining clonal resistance to PPR. A correlation coefficient of 0.59 (P<0.001) was obtained between the result of year-2 field observations and DPT-SM. Relatively lower correlation values were observed between DPT-SM and year-1 (r=0.55; P<0.001) and year-3 (r=0.44; P=0.005) field observations. The result of DPT-SM, however, shows a higher correlation (r=0.66; P<0.001) with the average of years 1-3 field observations. This suggests that a stronger association may exist between the result of DPT-SM and the cumulative data on field observations for a period longer than 3 years. The correlation (r=0.66; P<0.001) observed in this study confirms the usefulness of DPT-SM as an effective method of assessing clonal resistance to PPR and predicting field reaction in the long term. Since field observations are labour intensive and expensive to conduct on a yearly basis, the DPT-SM offers a cheaper and effective means of assessing clonal resistance to PPR. Being a non-destructive inoculation method, the DPT-SM provides a suitable option for cacao collections in genebanks to be assessed. It is also a cost-effective method for use in cacao breeding programmes. Based on its reliability, the DPT-SM has been