Genetic structure of Coffea canephora Pierre species assessed by microsatellites markers

Coffee is one of the most important cash crops for numbers of countries in the intertropical zones all over the world. Coffea canephora is responsible for about 35% of the total world production of coffee. Natural area of this species corresponds to the actual zone of tropical rainforest in Africa. In order to better assess genetic resources and natural history of this species, we analysed a sample of 285 individuals from different sampling points on the repartition area, including some cultivated genotypes. A set of 39 nuclear microsatellites markers was genotyped in order to investigate species genetic structure and population history. An integrate approach combining both distances (factorial analysis) and bayesian model (Structure) methods was used to study the species structure. We shown that 2 major groups can be clearly discriminated, those two groups correspond to previous work led by Berthaud. However a finest structure has been shown, dividing the previous groups in a total of 6 groups, whereas previous studies have shown 5). We tried to investigate those groups history by computing the dm² statistic of Goldstein in our sample. Results show the possible effect of glaciation refuge areas on the elaboration of the Coffea canephora genetic structure, separating a guinean region composed by 2 groups and a Congolese one composed by four groups

Daphne: a generic database to integrate multiscale agronomic and phenotypic information for crop modelling

Studies of genotype x environment x management (GXEXM) interactions commonly use Crop Simulation Models (CSM). The minimum datasets required for a successful model implementation are multi-scale, multi-species and multi-disciplinary. We observed that although they are organized differently, CSM input files and field experiment datasets shared the same measurements (yield, leaf area index, biomass, etc.) and a few similar tables corresponding to the minimum dataset (weather, soil, crop, and management data). Based on this analysis, we have designed the schema of DAPHNE. We used the relevant technology of metadata. Thus, in DAPHNE, all variable labels are stored in a metadata table including the units and methods of measurements and the observed and experimental units. The main advantage of this technology is that the addition of any variable does not imply to reconsider the structure of the database. Database query performance is also improved. DAPHNE already has a wide application in GXEXM experiments on sorghum and sugarcane. The genericness of the schema of DAPHNE can allow intercomparison of CSM that require the same datasets with no common data structure

Analysis of nucleotide diversity in Coffea spp. (W153)

Marker-assisted selection becomes a reality for many crops; in perennial crops, the utilization of molecular markers in breeding programs can speed up genotype selection. However, the most important commercial coffee species - allotetraploid C. arabica - has a restrict number of available polymorphic markers, which is a consequence of the narrow genetic basis and low molecular variability among cultivars. In order to study the nucleotide diversity in C. arabica, as well in other diploid Coffea relatives, we sequenced PCR amplified fragments of nine genes in 20 Coffea genotypes: twelve C. arabica, including eight wild genotypes and four commercial cultivars; and eight C. canephora genotypes. Genotypes of C. eugenioides, C. racemosa and Psylanthus bengalensis were also included in this analysis. From a total of 9 Kb analyzed, we found 573 polymorphisms: 500 SNPs; 39 INDELs and 34 SSRs. In C. canephora genotypes, we detected 188 polymorphisms (frequency of 2.09/100bp). For C. arabica we obtained similar results: 144 polymorphism (frequency of 2.13/100bp). Most of the polymorphism found in C. arabica only reflected the differences between ancestral homeologs, and they were monomorphic among different genotypes. However, 19 % of these polymorphisms (27 SNPs) were interespecific for C. arabica, and 13 of them were fixed among genotypes. The strategy of this work reflects the importance in using a more diverse panel of genotypes in order to identify SNPs in C. arabica, pointing out that the exploitation of wild germplasm will be an important source of genetic variability. (Résumé d'auteur

Analysis of DREB1D gene sequence in different Coffea genotypes : S03P07

In several plant species, the DREB genes play a key role in responses to abiotic stress. Since the development of molecular markers is one of the major goals for accelerating breeding programs, a study was done to evaluate the sequence variability of the DREB1D gene in several Coffea genotypes. The promoter and coding regions of this gene were cloned and sequenced from 16 coffee plants (including 10 from C. arabica and 4 from C. canephora), most of them characterized by different phenotypes (tolerance vs. susceptibility) regarding to drought. This showed that the DREB1D-coding sequence was highly conserved within coffee plants. However, several nucleic polymorphisms ("single nucleotide polymorphism" [SNP] and insertion/deletion [INDELs]) were found in the coffee DREB1D promoter regions. These polymorphisms could explained the differences of DREB1D gene expression levels previously observed in leaves of drought tolerant and susceptible clones of C. canephora. These polymorphisms also allowed the identification of different haplotypes like orthologous sequence variants (OSVs) of C. canephora and C. eugenioides as well as homologous single-nucleotide variants (HSVs) for C. arabica subgenomes (C. canephora and C. eugenioides) that could be used to develop allele and homoeologous specific markers for this locus. Work is now under way to evaluate the capacity of DREB1D promoter regions to control the expression of the uidA reporter gene in transgenic coffee plants. Work supported by CAPES-COFECUB, Consórcio Pesquisa Café and INCT-Café (CNPq/FAPEMIG). (Texte intégral

Identification des déterminants moléculaires de la qualité du café par des approches de génomique fonctionnelle. Une revue

La saveur du café implique le développement d'arômes lors de la torréfaction à partir de précurseurs biochimiques présents dans la graine de caféier. La caractérisation des voies de biosynthèse des principaux composés de réserve de la graine, ainsi que l'identification des gènes clés associés, permet donc d'identifier les déterminants moléculaires de la qualité. Cette revue décrit le développement récent des outils moléculaires et des connaissances génomiques chez le caféier. À travers la description des travaux de recherche ciblés sur la régulation du métabolisme des sucres, des acides chlorogéniques et de la caféine, les différentes approches de génomique fonctionnelle, et leurs complémentarités, sont illustrées. (Résumé d'auteur

Analysis of phenotypic plasticity in response to water constraints in coffee plants growing under field conditions

In a context of climate change, adaptation of perennial plantations to water constraints becomes a major concern for wood and fruit productivity. Adaptation depends on the level of genetic diversity in breeding and natural populations, as well as their plasticity. This project plans to describe adaptive mechanisms under water constraints for three perennial plants of temperate and tropical regions, including Pinus, Eucalyptus and Coffea, through a combined analysis of plant architecture, physiology, anatomy and molecular responses to drought stress. (Résumé d'auteur