Cacao breeding in Colombia, past, present and future

Cacao (Theobroma cacao L.) is considered a key crop in Colombian social programs aiming at alleviating rural poverty, promoting peace in post-conflict regions and, replacing crops used for illicit purposes. Colombia is thought to be part of the center of origin of cacao; several germplasm collecting expeditions have been implemented, dating back to the 1940s. Despite that history, the first breeding program based on creating, selecting, and releasing full-sib progenies made extensive use of accessions introduced from other countries as parents. A new breeding strategy was adopted in the 1990s, based on mass selection of promising trees (high-yield and disease-resistant) in farmers' fields, resulting in the selection of clones released to farmers as planting material. In 2012, a new strategy, Recurrent Selection, was adopted by the Colombian Corporation for Agricultural Research, Agrosavia, based on the development of improved populations and allowing the selection of clones at the end of each cycle of recombination. The use of molecular markers is being integrated into this program in order to assist breeders in selecting material. This review provides details about the history and perspectives of the cacao breeding program in Colombia.

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.

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.

Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions

BACKGROUND

Theobroma cacao L., is a tree originated from the tropical rainforest of South America. It is one of the major cash crops for many tropical countries. T. cacao is mainly produced on smallholdings, providing resources for 14 million farmers. Disease resistance and T. cacao quality improvement are two important challenges for all actors of cocoa and chocolate production. T. cacao is seriously affected by pests and fungal diseases, responsible for more than 40% yield losses and quality improvement, nutritional and organoleptic, is also important for consumers. An international collaboration was formed to develop an EST genomic resource database for cacao.

RESULTS

Fifty-six cDNA libraries were constructed from different organs, different genotypes and different environmental conditions. A total of 149,650 valid EST sequences were generated corresponding to 48,594 unigenes, 12,692 contigs and 35,902 singletons. A total of 29,849 unigenes shared significant homology with public sequences from other species.Gene Ontology (GO) annotation was applied to distribute the ESTs among the main GO categories.A specific information system (ESTtik) was constructed to process, store and manage this EST collection allowing the user to query a database.To check the representativeness of our EST collection, we looked for the genes known to be involved in two different metabolic pathways extensively studied in other plant species and important for T. cacao qualities: the flavonoid and the terpene pathways. Most of the enzymes described in other crops for these two metabolic pathways were found in our EST collection.A large collection of new genetic markers was provided by this ESTs collection.

CONCLUSION

This EST collection displays a good representation of the T. cacao transcriptome, suitable for analysis of biochemical pathways based on oligonucleotide microarrays derived from these ESTs. It will provide numerous genetic markers that will allow the construction of a high density gene map of T. cacao. This EST collection represents a unique and important molecular resource for T. cacao study and improvement, facilitating the discovery of candidate genes for important T. cacao trait variation.

Assessment of the value of doubled haploids as progenitors in cocoa (Theobroma cacao L.) breeding

In order to evaluate twelve doubled haploids (DHs) of Theobroma cacao L. used as parents, a trial was set up in Côte d'Ivoire. Several traits were observed, such as yield, vigour, yield/vigour ratios, resistance to the black pod disease caused by Phytophthora, percentage of flat beans and mean weight of 100 cocoa beans. Out of the three progenies derived from crosses between two DHs, two showed severe drawbacks. A reduction of the heterogeneity within these progenies was occasionally observed for some of the traits, but failed to be consistent. When tested as female parents in combination with diploid testers, some of the DHs showea significantly higher combining value than their parents for traits such as the mean weight of 100 beans and the yield/canopy surface ratio. The results showed the potential of DHs to improve selected parents in only one cycle of selection but more crosses between two DHs need to be tested in order to evaluate potential of the resulting F(1) progenies.