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

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

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

G2MARS a collaborative approach to improve fodder quality of European sorghum germplasm

The ability of sorghum to maintain a high level of biomass production in stressful environments makes it an interesting crop for animal feed as fodder, and for biomaterials and bioenergy production. Sorghum hybrids with improved agronomical behavior and high biomass quality are being developed for the European market. However the development of such hybrids requires a lot of field testing and biomass analyses. The current marker assisted breeding strategies offer the possibilities to better understand the genetic architecture of biomass quality and accelerate the creation of improved varieties. The G2MARS design developed in the frame of the “Biomass For the Future” project is gathering the know-how of both private companies and publics institutes to deliver new genetic marker and improved germplasm for the European biomass market. Seven biparental connected populations were developed in both genetic pools (3 in the male, 3 in the female and one male-female populations). These populations involved elite commercial cultivars and high biomass quality sorghum landraces. A total of 964 hybrids from these 7 populations were characterized in 2016 and 2017 in 2 locations. Agronomical traits and biomass quality related traits were measured. A QTL detection taking advantage of the connected design was performed with MCQTL and allowed the detection of 17 and 6 QTL respectively in the male and female pools. For each QTL the parental alleles were ranked allowing to define 2 target molecular ideotypes. The crossing strategy aiming to combine the most efficiently the favorable alleles was defined using Optimas. The G2MARS project offered the opportunity to take advantage of the specific skills of both private and public partners and develop a joint breeding action do develop hybrids suitable to fit the expectations of the biomass value chains. IN addition, this design improved the understanding of the genetic architecture of biomass quality traits that was mobilized to optimize the recombination strategy. This work was supported by the Biomass For the Future project (ANR-11-BTBR-0006-BFF) funded by the French National Research Agency (ANR)

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

Modeling the effect of soil meso- and macropores topology on the biodegradation of a soluble carbon substrate

Soil structure and interactions between biotic and abiotic processes are increasingly recognized as important for explaining the large uncertainties in the outputs of macroscopic SOM decomposition models. We present a numerical analysis to assess the role of meso- and macropore topology on the biodegradation of a soluble carbon substrate in variably water saturated and pure diffusion conditions . Our analysis was built as a complete factorial design and used a new 3D pore-scale model, LBioS, that couples a diffusion Lattice-Boltzmann model and a compartmental biodegradation model. The scenarios combined contrasted modalities of four factors: meso- and macropore space geometry, water saturation, bacterial distribution and physiology. A global sensitivity analysis of these factors highlighted the role of physical factors in the biodegradation kinetics of our scenarios. Bacteria location explained 28% of the total variance in substrate concentration in all scenarios, while the interactions among location, saturation and geometry explained up to 51% of it

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

Phenotypic analysis of Coffea arabica accessions from Ethiopia: Contribution to the undestanding of Coffea arabica diversity

As a consequence of Coffea arabica domestication process, the genetic diversity of cultivated genotypes of this species is extremely restricted. According to this observation, FAO organized, in 1964-1965, surveys of spontaneous and subspontaneous genotypes in the main center of origin (Ethiopia). Various studies were performed regarding the phenotypic variability of these accessions. However a clear understanding of the structure of the phenotypic diversity in Ethiopia remains to be reached. We present here the phenotypic analysis of 130 Ethiopians accessions with 37 phenotypic traits. Two main goals were pursued: to evaluate the interest of Ethiopian accessions for Coffea arabica breeding, and to test relationships between phenotypic variability and geographic origins. (Résumé d'auteur

The road to sorghum domestication: evidence from nucleotide diversity and gene expression patterns. P1159

Sorghum bicolor is the fifth cereal worldwide for grain production, constituting the staple food for a round 500 million people. The release of its genome sequence, its phylogenetic proximity with other important C4 species (maize, switchgrass, sugarcane) and its low genome complexity contribute to its interest on a more fundamental level. Sorghum bicolor wild relatives (ssp. verticilliflorum) and domesticated (ssp. bicolor) pools are inter-fertile and intense gene flow occurs. However, a clear domestication syndrome is visible (plant architecture, shattering, dormancy and seed weight). ln spite of its agronomical Importance, the evolutionary dynamics of sorghum domestication and the genetic bases of adaptations to natural and anthropogenic pressures are not well understood. Here we leverage transcriptomic and genomic resources to improve our knowledge on the evolutionary history of S. bicolor, with a particular focus on the consequences of the domestication process. As a first step, gene expression and nucleotide variability of the expressed genes were analyzed in 11 cultivated and 9 wild accessions selected to maximize the genetic coverage of these two pools. The cultivated compartment harbors 30% lower genetic diversity than the wild pool, which supports the occurrence of a genetic bottleneck in the domestication history of sorghum. More than 900 genes are significantly differentially expressed between the two compartments. Among them, genes involved in photosynthesis and in reduction-oxidation processing of seed storage proteins are over-represented. Further analyses revealed that domestication reduced significantly the variability of the isoform expression balance (expression ratio of the alternative proteins coded by a single gene) in cultivated sorghum. Scans for local adaptation and positive selection on large cultivated and wild panels genotyped with genotyping by sequencing approaches are ongoing. Overall, these analyses pave the way towards the identification of key domestication genes that cou Id be useful for conservation strategies but also for breeding purposes