Selfing of Self-Incompatible Cocoa

Deciphering the Theobroma cacao self-incompatibility system: from genomics to diagnostic markers for self-compatibility

Cocoa self-compatibility is an important yield factor and has been described as being controlled by a late gameto-sporophytic system expressed only at the level of the embryo sac. It results in gametic non-fusion and involves several loci. In this work, we identified two loci, located on chromosomes 1 and 4 (CH1 and CH4), involved in cocoa self-incompatibility by two different processes. Both loci are responsible for gametic selection, but only one (the CH4 locus) is involved in the main fruit drop. The CH1 locus acts prior to the gamete fusion step and independently of the CH4 locus. Using fine-mapping and genome-wide association studies, we focused analyses on restricted regions and identified candidate genes. Some of them showed a differential expression between incompatible and compatible reactions. Immunolocalization experiments provided evidence of CH1 candidate genes expressed in ovule and style tissues. Highly polymorphic simple sequence repeat (SSR) diagnostic markers were designed in the CH4 region that had been identified by fine-mapping. They are characterized by a strong linkage disequilibrium with incompatibility alleles, thus allowing the development of efficient diagnostic markers predicting self-compatibility and fruit setting according to the presence of specific alleles or genotypes. SSR alleles specific to self-compatible Amelonado and Criollo varieties were also identified, thus allowing screening for self-compatible plants in cocoa populations.

Understanding the genetic diversity, spatial genetic structure and mating system at the hierarchical levels of fruits and individuals of a continuous Theobroma cacao population from the Brazilian Amazon

Understanding the mating patterns of populations of tree species is a key component of ex situ genetic conservation. In this study, we analysed the genetic diversity, spatial genetic structure (SGS) and mating system at the hierarchical levels of fruits and individuals as well as pollen dispersal patterns in a continuous population of Theobroma cacao in Pará State, Brazil. A total of 156 individuals in a 0.56 ha plot were mapped and genotyped for nine microsatellite loci. For the mating system analyses, 50 seeds were collected from nine seed trees by sampling five fruits per tree (10 seeds per fruit). Among the 156 individuals, 127 had unique multilocus genotypes, and the remaining were clones. The population was spatially aggregated; it demonstrated a significant SGS up to 15 m that could be attributed primarily to the presence of clones. However, the short seed dispersal distance also contributed to this pattern. Population matings occurred mainly via outcrossing, but selfing was observed in some seed trees, which indicated the presence of individual variation for self-incompatibility. The matings were also correlated, especially within (Ρ(p(m))=0.607) rather than among the fruits (Ρ(p(m))=0.099), which suggested that a small number of pollen donors fertilised each fruit. The paternity analysis suggested a high proportion of pollen migration (61.3%), although within the plot, most of the pollen dispersal encompassed short distances (28 m). The determination of these novel parameters provides the fundamental information required to establish long-term ex situ conservation strategies for this important tropical species.

Parentage analysis and outcrossing patterns in cacao (Theobroma cacao L.) farms in Cameroon

The present study investigates the parentage of farm accessions in Cameroon using data from 12 microsatellite loci. Bayesian analysis suggests that 25.5% of the 400 farm accessions studied is still closely related to the traditional Amelonado variety called 'German Cocoa' by the farmers. Another 46.3% of the farm accessions were found to be direct descendants (20.8% first-generation (F1) hybrids and 25.5% selfed genotypes) from 24 parental clones used in biclonal seed gardens (BSGs) established in the 1970s in southern and western Cameroon. Furthermore, 28.3% of farm accessions appeared to descent from uncontrolled pollination events in cacao farms, which could be related to a common practice of cacao growers to use seeds collected in their own farm for new plantings. All farm accessions descending from BSG could be individually related through parentage analysis to the 24 progenitors of the BSG. Only 25% of progenies distributed from BSG corresponded to F1 hybrids combinations originally planned to be released. Significant biparental inbreeding estimates were observed for all 'traditional' farms and for most 'F1 hybrids' farms due to presence of a high proportion of selfed accessions. Biparental inbreeding occurs when plants receive pollen from genetically related neighbors. High levels of outcrossing observed in 'mixed' farms might be explained by the admixture of traditional varieties and BSG progenies. The implications of our finding for management of seed gardens and for further breeding using farm accessions in Cameroon are discussed.

Ecophysiology of the cacao tree

Cacao, one of the world's most important perennial crops, is almost exclusively explored for chocolate manufacturing. Most cacao varieties belong to three groups: Criollo, Forastero and Trinitario that vary according to morphology, genetic and geographical origins. It is cropped under the shade of forest trees or as a monocrop without shade. Seedlings initially show an orthotropic growth with leaf emission relatively independent of climate. The maturity phase begins with the emission of plagiotropic branches that form the tree crown. At this stage environmental factors exert a large influence on plant development. Growth and development of cacao are highly dependent on temperature, which mainly affects vegetative growth, flowering and fruit development. Soil flooding decreases leaf area, stomatal conductance and photosynthetic rates in addition to inducing formation of lenticels and adventitious roots. For most genotypes drought resistance is associated with osmotic adjustment. Cacao produces caulescent flowers, which begin dehiscing in late afternoon and are completely open at the beginning of the following morning releasing pollen to a receptive stigma. Non pollinated flowers abscise 24-36 h after anthesis. The percentage of flowers setting pods is in the range 0.5 - 5%. The most important parameters determinants of yield are related to: (i) light interception, photosynthesis and capacity of photoassimilate distribution, (ii) maintenance respiration and (iii) pod morphology and seed fermentation, events that can be modified by abiotic factors. Cacao is a shade tolerant species, in which appropriate shading leads to relatively high photosynthetic rates, growth and seed yield. However, heavy shade reduces seed yield and increases incidence of diseases; in fact, cacao yields and light interception are tightly related when nutrient availability is not limiting. High production of non-shaded cacao requires high inputs in protection and nutrition of the crop. Annual radiation and rainfall during the dry season explains 70% of the variations in annual seed yields.

Mentor pollen effects on gametophytic incompatibility in Nicotiana, Oenothera and Lycopersicum

Attempts were made, through mentor pollen techniques, to overcome self-incompatibility in species belonging to the genera Nicotiana and Oenothera and in a hybrid of Lycopersicum, which are characterized by a gametophytic system of incompatibility. While radiation-killed incompatible pollen did not generate mentor effects in any of the material tested, radiation-killed compatible pollen was found to promote a high level of illegitimate fertilizations by incompatible pollen in N. alata. No evidence was obtained that radiation-killed compatible pollen could induce mentor effects in strictly self-incompatible clones of O. organensis and of the interspecific hybrid L. esculentum x L. peruvianum.