Genetic diversity and population structure in wild stands of cacao trees (Theobroma cacao L.) in French Guiana

The native cacao trees (Theobroma cacao L.) in south-eastern French Guiana represent a noteworthy fraction of the genetic diversity of this species. Several scientific surveys have led to the collection of numerous accessions, which provides an opportunity for investigating the pattern of genetic diversity in natural populations. Using a capillary electrophoresis genotyping system, we fingerprinted 189 wild trees in 18 natural populations. Based on the 15 loci SSR profiles, we analyzed the intra- and inter-population variation and their relationship with control clones. The global allelic richness was 4.87 alleles per locus, but was 2.4 on average within individual populations; gene diversity was 0.368 and observed heterozygosity was low (0.160). Major structuring was discovered in the metapopulation of French Guianan wild cacao trees (Fst = 0.20), which could be explained by the biological characteristics of the cacao tree and the climatic events that affected the Guianan forests in the Quaternary period.     

Twenty years of agronomic evaluation of wild cocoa trees (Theobroma cacao L.) from French Guiana

Almost 500 clones of wild cocoa trees (Theobroma cacao L.) grown from pods collected in 1987 from wild mother-trees in the Camopi and Tanpok river basins (southeastern French Guiana) have been distributed in around fifteen cocoa producing countries since 1988. The name of those clones always bears the GU prefix (for “Guyane”, i.e. French Guiana). All the germplasm of the same geographical origin present in the CIRAD collection at Paracou-Combi (Sinnamary, French Guiana), i.e. more than 1600 trees, has been abundantly studied for its morphological characterization, its agronomic assessment or its genetic diversity. Other assessment work, primarily on resistance to certain diseases, has been carried out by CIRAD in Montpellier, or in various countries by other organizations.     

The Criollo cacao tree (<Emphasis Type="Italic">Theobroma cacao</Emphasis> L.): a review

In commercial terms, Criollo cacao trees (Theobroma cacao L.) are reputed to be the source of the commercial product (fermented and dried cocoa beans), which sells for the best price on the market. Nevertheless, the term “Criollo” has numerous meanings and interpretations depending on if it is used by commercial users or botanists, growers or breeders. Our review aims to specify which cocoas can justifiably carry the Criollo name. “Criollo” is a botanical subspecies of Theobroma cacao, i.e. Theobroma cacao subsp. cacao; however, the true Criollos form just one of the ten currently accepted genetic groups in the species. We thus provide an overview of genetic studies on the subject (published or not), along with what is currently known about “True Criollo” or “Ancient Criollo” cacao trees. In fact, there are few representatives in collections that are duly acknowledged to be true Criollos, particularly in the two International Cocoa Genebanks, where only seven clones are available. It is nonetheless certain that some true Criollos do exist in other collections but have not been formally identified (by genetic studies) as members of the Criollo genetic group. Likewise, some true Criollos, be they cultivated or subspontaneous, exist in Mexico and Central and South America (Venezuela and Colombia). However, certain clones called “modern Criollos”, which are closely related to the true Criollos but arise from hybridization with other genetic groups, are more common.     

New sources of resistance to Phytophthora megakarya identified in wild cocoa tree populations of French Guiana

Cocoa black pod rot, a disease caused by oomycetes of the genus Phytophthora, causes substantial yield losses throughout the world, particularly in Africa with the very aggressive species Phytophthora megakarya. In order to reduce the impact of that pathogen, priority is given to genetic control through more resistant cultivars, and breeders are seeking sources of resistance in wild cocoa trees. Wild cocoa trees were surveyed in French Guiana between 1985 and 1995, leading to the collection of abundant plant material from more than 200 mother trees originating from five river basins. We present here the results of tests to assess resistance to the species P. megakarya (a species only existing in Africa), conducted at CIRAD in Montpellier, France, on circa 40 genotypes collected in the Camopi river basin, along with approximately 20 genotypes from other populations (Kérindioutou, Borne 7, Euleupousing, Pina and Oyapok). The strain used for artificial inoculation was NS269, isolated in Cameroon. Seven cacao clones were classified as “highly resistant” and 29 as “resistant”, some of which displayed greater resistance to P. megakarya than the reference resistant clone IMC 47. This study suggests that the wild material from French Guiana could play a significant role in controlling P. megakarya in Africa and also Phytophthora palmivora in all cocoa-producing zones.     

Competition effects in cocoa (Theobroma cacao L.) hybrid trials

A method developed in coffee tree breeding to assess family competitioneffects (partner effects) in comparative variety trials was applied to thecocoa tree (Theobroma cacao L.). The study was conducted in ahybrid comparative trial planted in French Guiana, involving twelve familiesof 50 trees in a totally randomized single-tree plot design, at a density of1,667 trees per hectare. The trial was thinned at 10 years, at a rate of twoout of four rows. Competition was studied with reference to juvenile andadult vegetative vigour, and to periodic and cumulative yields (number ofpods, potential weight, average weight of one pod, and the production:vigour ratio). At the end of the trial, after thirteen years of monitoring,competition effects were revealed which explained 8 to 10% of theresidual variance after removal of the hybrid and micro-environment effects.These effects, which were detected as early as 18 months, occurred earlierthan generally acknowledged. Under the trial conditions, the families couldbe classed as aggressive, stimulating or passive for their neighbours.Vegetative vigour (trunk cross-section) explained 34% of the competitioneffects (partner effects), which, with hindsight, vindicated the use of theproduction : vigour ratio as the main selection criterion in cocoa breeding.The partner effects noted on the production variables were never explainedby any production variable, hence non-aggressive high-yielding families canbe selected.     

Variations in the number of beans per pod in Theobroma cacao L. in the Ivory Coast. I. The role of pollen

Incomplete pod filling is frequently encountered in cocoa cultivation, but there is disagreement as to the causes. Pollen factors (amount and quality of pollen) were studied on several clones in the Ivory Coast. Hand pollination with compatible pollen showed that the pod filling of clone UPA 413 can be improved, but not that of clone SCA 6. The pollen genotype, and not just its compatibility, seems to affect the average number of beans per pod, but not the standard deviations. Experiments on the number of pollen grains deposited (pollination) looked at hand pollination (where there is always excess pollen), the life span of flowers depending on pollination conditions and the amount of pollen in fallen flowers. They showed that hand pollination with compatible pollen does not always guarantee complete pod filling, that many flowers pollinated with clusters of pollen can fall and that large amounts of pollen are required to obtain pods.     

Genetic diversity and parentage in farmer varieties of cacao (Theobroma cacao L.) from Honduras and Nicaragua as revealed by single nucleotide polymorphism (SNP) markers

Cacao (Theobroma cacao L.) is the main source for chocolate with an annual production of four million tons worldwide. This Neotropical tree crop was domesticated in Mesoamerica as far back as 3,000 years ago. Knowledge of genetic diversity and population structure in farmer varieties of cacao in the center of domestication is essential for sustainable production of fine-flavored cacao beans and contributes to in situ/on-farm conservation of farmer varieties. Based on 70 single nucleotide polymorphism markers, we analyzed 84 fine-flavored farmer varieties collected from traditional cacao farms in Honduras and Nicaragua. The study also included 31 clones from the international cacao collections to serve as references. The SNP based multilocus matching identified six synonymous groups, including 14 Criollo and two Amelonado varieties. A moderately high level of genetic diversity was observed in these farmer varieties, indicating the possibility to further explore intra-population variation and breed for fine-flavored cocoa. Multivariate analysis showed clustering of the 84 farmer accessions in five genetic groups: ancient Criollo, Amelonado, Trinitario (including Nicaragua Trinitario and Honduras Trinitario) and Upper Amazon Forastero (only one accession). The Honduras Trinitario differed from the Nicaragua Trinitario group. The clustering results largely supported the perceived classification of cacao by local farmers and researchers, which was mainly based on morphological traits. However, the well known traditional variety “Indio” in this region was identified as synonymous with Amelonado. Parentage analysis showed that the variety “Indio” (or Amelonado) contributed more to the Trinitario type farmer varieties, whereas ancient Criollo had less influence. The present study demonstrates the efficacy of using a small set of SNP makers for cacao germplasm characterization, and further depicts the diverse origins and parentage in farmer varieties from Mesoamerica. This information thus will be highly useful for conservation and utilization of cacao germplasm from this region.