Cocoa

Plant animator: Xavier Argout
xavier.argout@cirad.fr

Maintaining the flavour qualities of fine cocoas (Nacional and Criollo), a veritable economic challenge for some cocoa producing countries, and establishing, in the cacao tree, production levels and durable resistance to diseases (Phytophthora, witches’ broom), which are responsible for over 30% of harvest losses, are the main research objectives worked on by the team for this species. To achieve those objectives, different approaches are taken and integrated, from sequencing to genome analysis, and including the collection and exploitation of native genetic resources.

In recent years, the genetic bases (QTLs) of many traits have been analysed and synthesized. For traits of resistance to diseases, in particular, they have been accompanied by functional genomics studies providing a better understanding of the mechanisms involved in resistance to witches’ broom and Phytophthora. Some new selection strategies, such as genomic selection, have been implemented working with several Southern partners to optimize selection strategies. The founding of an international consortium, coordinated by the team, led to the sequencing of the cacao genome (Criollo variety) and the identification of 28,798 genes that have been annotated. Among them, several families of genes linked to quality and disease resistance traits have been identified, mapped on the genome sequence and compared to the QTLs identified for those traits. A large number of candidate genes have been identified in that way, some of which are currently undergoing functional studies to confirm their involvement in the variation of the target traits.

A study on the domestication of flavour cocoa varieties (Nacional) in recent years helped to identify the region of origin of its domestication. These results led on to a survey of native cacao trees in the previously identified domestication region. The collections established help to enrich these genetic resources and start to exploit them to genetically improve the Nacional variety.

Coffee

Our team is working on the genetic diversity of coffee trees (C. canephora and C. arabica) and the selection of productive coffee trees that yield quality coffee and are tolerant of biotic and abiotic stresses. Quantitative genetics and genomics tools are used to:

• manage genetic resources in the field, notably at the CIRAD Biological Resource Centre in French Guiana,
• genetically improve C. canephora (and C. eugenioides): genetic diversity studies on the species in core collections, studies of linkage disequilibrium, QTL searches, selection of high-yielding genotypes in Ivory Coast, Uganda, Ecuador, French Guiana, and molecular analyses of the whole genome,
• genetically improve C. arabica: diversity of collections with Brazil and Cameroon, search for selection markers, genetic mapping, and definition of a plan to revive coffee growing in Cameroon.
• genetically improve the C. arabusta hybrid in French Guiana with the selection of hybrids adapted to its agroclimatic conditions and the creation of a coffee supply chain.

Rubber

Plant animator: A. Clément-Demange
andre.clement-demange@cirad.fr

Natural rubber production in the world is almost exclusively provided by Hevea plantations, be they estates (20% of the areas) or smallholdings (80%). Rubber genetics research therefore seeks to create new Hevea cultivars that are well adapted to the growing regions, and maximize rubber production per unit of time, space and labour. In this context, we focus our work on a few key points, namely: (i) characterizing the genetic diversity of natural Hevea populations and its dynamic management in ex situ conservation centres; (ii) understanding interaction mechanisms with two major fungal diseases (Microcyclus ulei and Corynespora cassiicola) to create resistant cultivars; (iii) developing new molecular marking technologies and new strategies for optimizing breeding efficiency; (iv) in partnership with the Institut Français du Caoutchouc (IFC), setting up and running an experimental variety creation network in West Africa, based on early selection trials with a view to creating clones adapted to these high-potential regions; (v) moving on to the pre-development phase for some genotypes created in Brazil as part of a CIRAD-Michelin-Brazil project over the last 20 years. Efforts are currently being made to characterize the rubber quality of the most widely cultivated clones and of some experimental clones in large-scale trials amounting to the final assessment of the clones.

Plantation forest species

Eucalyptus, Pinus, Acacia

Plant animator: J-M Gion
jean-marc.gion@cirad.fr

Tectona

Plant animator: O. Monteeuis
olivier.monteuuis@cirad.fr

In the climate change context, studying the genetic and environmental determinism of traits of economic and adaptive interest in plantation trees is a response to the major challenge of sustainably producing a renewable resource such as wood. The team is involved in research on the four forest species most frequently planted worldwide: Eucalyptus, Pinus, Acacia and Tectona.

The scientific objectives are to identify the genetic and environmental factors of wood production (in quantitative and qualitative terms). A large share of the work focuses on analysing the genetic architecture (QTL) of growth traits, wood quality traits and traits of the response to abiotic stress, etc. The existence of reference genomes and the use of so‑called high throughput technologies to characterize both genotypes (nucleotide polymorphisms) and phenotypes (real-time data), offer new prospects for analysing genotype x environment interactions, an essential component of the plasticity of phenotypes of interest. The identification of genes underlying QTLs, the analysis of their expression in varied environmental contexts and their regulation (including epigenetic) all amount to information likely to enrich and thereby improve genomic prediction models. These genomic prediction models seek to, i/ understand the biological processes brought into play along with the different scales of interaction, and ii/ use that information to select the forest genotypes best suited to the targeted silviculture models.

A developmental component - phase changes - is addressed, notably to guarantee the clonal propagation ability of selected genotypes, and thereby ensure their dissemination by herbaceous cuttings. Our multidisciplinary approaches combine phenotyping in the field, genomics, modelling and biostatistics. We take an integrated approach to the issues of diversity, quantitative genetics, plant functioning, modelling, combining molecular tools, phenotyping and agronomy trials.

Oil palm

Plant animator: Teresa Cuellar
teresa.cuellar@cirad.fr

The merits of the oil palm (Elaeis guineensis Jacq.) primarily lie in its richness in palm oil contained in the mesocarp of its fruits produced throughout the year. The oil palm is the world’s leading source of fats and oils (30%) with a productivity that is unrivalled by the other oilcrops (soybean, sunflower, rapeseed).

The genetic and molecular control of its traits of agronomic interest for breeding (palm oil production and quality, disease resistance) is studied with partners in Africa, Southeast Asia and South America. This work involves taking original genetic approaches seeking to make use of the experimental designs of breeding programmes in which numerous progeny tests are carried for parents of known pedigree. This approach has proved particularly effective in identifying QTLs (quantitative trait loci) that are useful in breeding and it can be generalized to other species which encounter the same scientific problems as the oil palm. In addition, studies combining the structural approach and functional genomics lead on to the identification of the genes involved.

The use of molecular markers to study and genetically improve the oil palm has been stepped up since 2010, mostly thanks to the identification of the regions of the genome responsible for phenotypic variations (QTLs), as a public sequence of the whole genome has been available since 2013, and because some major molecular resources of the transcriptome and whole genome have been developed by the Oil Palm Genome Projects (OPGP) International Consortium coordinated by the team. The identification of QTLs controlling traits involved in yields has benefited from the originality of an approach adapting methods derived from both human and animal research, based on knowledge of pedigrees over several generations. Statistical modelling then makes it possible to link parental genetic information with the phenotypic information of progenies using a mixed linear model. The major merits of this approach lie in the gain in power and relevance of the QTLs directly transferrable for marker-assisted selection, applied in particular to the genomic selection model.

Predictive epidemiology, molecular plant pathology and population genetics are the drivers within the team for gaining a basic understanding of plant-pathogen interactions so as to more effectively find the genetic and agroecological determinants of oil palm resistance to the main diseases, with a view to integrated, ecofriendly biological control of Fusarium vascular wilt, the main fungal disease in Africa, the fungus Ganoderma boninense in Southeast Asia, and Bud Rot, mainly described in Latin America. In addition to creating resistant varieties, these studies are intended to develop disease management methods during the cropping cycle that are more supervised and environment-friendly.