A global strategy for the conservation and use of cacao genetic resources, as the Foundation for a sustainable cocoa economy

The future of the world cocoa economy depends on the availability of genetic diversity and the sustainable use of this broad genetic base to breed improved varieties. Decreasing cacao genetic diversity (in situ, on-farm and conserved in collections) is a serious problem and all its many causes need to be urgently addressed: the destruction of the Amazonian rainforests, changing patterns of land use, the spread of pests and diseases, sudden changes in climate, and threats from natural disasters and extreme weather. These factors are resulting in an irreversible loss of the cacao genetic diversity so essential for farmers, breeders, and consumers. Most of the countries involved in the improvement and production of cacao are highly dependent on genes and varieties characterized and conserved in other countries and regions. Effective management of cacao genetic resources can therefore only be carried out through international collaboration. A considerable portion of the global cacao diversity is in situ, in farmers' fields and held in genebanks around the world, including two international collections maintained at the Cocoa Research Centre of the University of the West Indies (CRC/UWI), Trinidad and Tobago, and at the Centro Agronómico Tropical de Investigación y Enseñanza (CATIE), Costa Rica. Unfortunately, much of the genetic resources maintained in national collections is under-used or at risk, and funding remains insufficient and unstable. The vision of the Global Strategy for the Conservation and Use of Cacao Genetic Resources is to improve the livelihoods of the 5-6 million farmers in developing countries across tropical Africa, Asia and Latin America and the 40-50 million people who depend upon cocoa for their livelihoods. The specific goal is to optimize the conservation and maximize the use of cacao genetic resources as the foundation of a sustainable cocoa economy. This it does by bringing together national and international players in public and private sectors. The expected outputs are: (1) the cacao genepool is conserved in situ and ex situ for the long term by a global network of partners, (2) the global system for the safe exchange of cacao germplasm is strengthened, (3) the use of cacao genetic diversity is optimized and (4) the effectiveness of global efforts to conserve and use cacao genetic resources is assured. To ensure these outputs are implemented, the first and urgent task will be to secure funding for the existing cacao genetic diversity currently maintained in ex situ collections and accessible in the public domain. CacaoNet will work towards the establishment of an endowment fund for the conservation and use of the most valuable resources in perpetuity. At the centre of the Global Strategy is the Global Strategic Cacao Collection (GSCC): a "virtual genebank" of accessions of highest priority for conservation, wherever they are physically located. The accessions will be selected to capture the greatest range of genetic (allelic) richness and key traits of interest to users. The inclusion of materials in the GSCC will be on the basis that governments concerned will be willing to place them in the public domain, and will take the necessary political and legal steps to do so and thus to make this material available to users worldwide. The Global Strategy, developed by the Global Network for Cacao Genetic Resources (CacaoNet), is the result of a consultation process that drew upon the global cocoa community's expertise in all aspects of cacao genetic resources. It provides a clear framework to secure funding for the most urgent needs to ensure that cacao diversity is conserved, used and provides direct benefits to the millions of small-scale cacao farmers around the world. (Résumé d'auteur

High throughput, high resolution selection of polymorphic microsatellite loci for multiplex analysis

Background Large-scale genetic profiling, mapping and genetic association studies require access to a series of well-characterised and polymorphic microsatellite markers with distinct and broad allele ranges. Selection of complementary microsatellite markers with non-overlapping allele ranges has historically proved to be a bottleneck in the development of multiplex microsatellite assays. The characterisation process for each microsatellite locus can be laborious and costly given the need for numerous, locus-specific fluorescent primers. Results Here, we describe a simple and inexpensive approach to select useful microsatellite markers. The system is based on the pooling of multiple unlabelled PCR amplicons and their subsequent ligation into a standard cloning vector. A second round of amplification utilising generic labelled primers targeting the vector and unlabelled locus-specific primers targeting the microsatellite flanking region yield allelic profiles that are representative of all individuals contained within the pool. Suitability of various DNA pool sizes was then tested for this purpose. DNA template pools containing between 8 and 96 individuals were assessed for the determination of allele ranges of individual microsatellite markers across a broad population. This helped resolve the balance between using pools that are large enough to allow the detection of many alleles against the risk of including too many individuals in a pool such that rare alleles are over-diluted and so do not appear in the pooled microsatellite profile. Pools of DNA from 12 individuals allowed the reliable detection of all alleles present in the pool. Conclusion The use of generic vector-specific fluorescent primers and unlabelled locus-specific primers provides a high resolution, rapid and inexpensive approach for the selection of highly polymorphic microsatellite loci that possess non-overlapping allele ranges for use in large-scale multiplex assays

Tackling mislabelling in cocoa germplasm collections

The level of mislabelling of cocoa clones in germplasm collections is fairly high. Although not a new problem, the availability of genetic fingerprinting technologies has allowed projects to be developed that use microsatellite markers to compare clones. However, it is important that when clones with the same name are found to have different profiles, one is determined to be the true type (with reference to the most original material). Off-types should be kept for their potential agronomic value, but with a unique new name. We have proposed a format for renaming that highlights the mislabelling event and which includes references to the source germplasm collection and the name originally given to the clone. (Résumé d'auteur