Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Identification of duplicates for the optimization of carrot collection management

International audienceMolecular markers have proved their efficiency for the identification of duplicate accessions in genetic resources collections. Partners of the GENRES Carrot project decided to evaluate the use of molecular markers for the identification of carrot accession duplicates. As a model analysis, 21 presumed duplicate accessions of lsquoJaune du Doubsrsquo were selected. Only accessions that were not distinguished on a morphological basis were subjected to molecular analysis. The crucial question was to determine the threshold required to declare whether accessions were duplicates or not. We used a strategy based on the comparison between intravarietal and intervarietal genetic distances. DNA extractions were made on 4–8 bulks of five individuals per accession, and the bulks were analysed using 75 AFLP markers. An additional set of 7 bulks was extracted from one accession to provide true control replicates. With the exception of the true duplicates, all the accessions were clearly differentiated. Based on these results, a general strategy for the identification of carrot duplicates is proposed

Indicators to assess temporal genetic diversity in the French Catalogue: no losses for maize and peas

International audienceThe aim of this study, led by the GEVES (Research and Control Group for Varieties and Seeds), was to suggest indicators to assess the diversity available to farmers since the French Official Catalogue for Plant Varieties and Species was initiated. The largest datasets of 1990 inbred maize lines and 578 pea lines from the last 50 years were analysed using morphological and enzymatic parameters. Lines were grouped into three to five periods. Genetic diversity was estimated in each period from morphological and enzymatic markers by computing numerous indices, such as the number of classes of scores for each characteristic, allelic richness or genetic diversity index (H (e) ). Population differentiation parameters (G(ST), G(ST)', F-ST, Q(ST)) were also estimated between periods. While genetic diversity computed from distinction, uniformity, stability traits was more marked for maize (0.66) than for garden peas (0.35) or feed peas (0.29), the opposite trend was observed with enzymes, resulting in a genetic diversity of 0.43, 0.35 and 0.22 for garden peas, feed peas and maize, respectively. However, no significant changes in genetic diversity were observed over time, and genetic differentiation was slight between periods. All our results demonstrated that no significant reduction in the diversity available to farmers had been observed since initiation of the French Catalogue. The H (e) was a good indicator providing a quantitative estimate of genetic diversity, but it should be interpreted alongside a more precise indicator such as allelic richness or the number of classes for morphological characteristic

Genetic resources management with networks: the example of the network "Carrot and other Daucus"

International audienceAs for many other species, the request of the producers, distributors and consumers for more homogeneous and more uniform products in carrot resulted in a considerable reduction of the number of cultivated varietal types. In order to face this possible genetic erosion, actions of conservation were committed in the world. In a majority of countries, these actions are concentrated within organizations such as multi-species gene banks. On the contrary, the French organization is based on networks specialized in a species or group of species. The Office of Genetic Resources (BRG) ensures the coordination of these networks. The network "Carrot and other Daucus" was created in 1996, and involves research institutes, seed companies, experimental and technical agencies as well as botanical gardens or amateurs, all experts of the carrot species. Each year, about 40 accessions are characterized and 5 to 10 accessions to be introduced in the national collection are regenerated. In accordance, the objectives of the network are to gather, evaluate, preserve the old carrot varieties and related species, and thus to contribute to the safeguard, verification and diffusion of the French genetic inheritanc

Impact of carrot resistance on development of the Alternaria leaf blight pathogen (Alternaria dauci)

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699International audienceThe interaction between Alternaria dauci and two carrot cultivars differing in their resistance to leaf blight was investigated by microscopy. The fungal development between 1 and 15 days post-inoculation was quite similar in the susceptible cv. Presto and the partially resistant cv. Texto: After conidial germination, leaf adhesion of the pathogen was achieved with mucilaginous filaments; hyphae penetrated the leaves directly with/without the formation of appressoria-like structures or via stomata; the fungus spread by epiphytic hyphae with hyphopodia and subcuticular mycelia. Intense necrotic plant cell reactions occurred under the fungal structures. At 21 days post-inoculation, typical features of fungal development were noted for each cultivar: growing hyphae emerged from stomata in cv. Presto, whereas conidiophores without conidia were observed in cv. Texto. Leaf tissues of both cultivars were strongly damaged and vesicle-like structures (assumed to be plant phenolics) were abundantly present between mesophyll cells. A real-time PCR method was developed for in planta quantification of A. dauci. Between 1 and 15 days post-inoculation, the fungal biomass was equivalent in the two cultivars and was about fourfold higher in cv. Presto than cv. Texto at 21 and 25 days post-inoculation. Taken together, our results indicated that A. dauci was able to colonize both cultivars in a similar manner during the first steps of the interaction, then fungal development in the partially resistant cultivar was restricted due to putative plant defence reactions. The results of this study enhance the overall understanding of infection processes in the A. dauci-carrot pathosyste

Comment mesurer la résistance quantitative de la carotte à Alternaria dauci ? Comparaison de différentes méthodes.

National audienc

Carrot resistance to Alternaria leaf blight: from genetics to metabolomics

International audienc

Link between carrot leaf secondary metabolites and resistance to Alternaria dauci

Alternaria Leaf Blight (ALB), caused by the fungus Alternaria dauci, is the most damaging foliar disease affecting carrots (Daucus carota). In order to identify compounds potentially linked to the resistance to A. dauci, we have used a combination of targeted and non-targeted metabolomics to compare the leaf metabolome of four carrot genotypes with different resistance levels. Targeted analyses were focused on terpene volatiles, while total leaf methanolic extracts were subjected to non-targeted analyses using liquid chromatography couple to high-resolution mass spectrometry. Differences in the accumulation of major metabolites were highlighted among genotypes and some of these metabolites were identified as potentially involved in resistance or susceptibility. A bulk segregant analysis on F3 progenies obtained from a cross between one of the resistant genotypes and a susceptible one, confirmed or refuted the hypothesis that the metabolites differentially accumulated by these two parents could be linked to resistance

Combined Alternaria dauci infection and water stresses impact carotenoid content of carrot leaves and roots

Carotenoids are important secondary metabolites involved in plant photosynthesis, vegetable nutritional quality but also in metabolic prevention in human health. Carrot represents one of the most important carotenoid intakes and is a very interesting model to study carotenoid metabolism. Till now, the knowledge about the impact of stress on carotenoid accumulation is limited. The purpose of this work was to investigate the impact of abiotic and biotic stresses applied separately or in combination on carotenoid accumulation in carrot leaves and roots. Results showed that combined stress decreased dramatically carotenoid content in both organs. In roots, the decrease in carotenoid content could be mostly associated in carrot response to A. dauci infection. Moreover, carotenoid and sugar contents were highly correlated, which suggests that stored metabolites are directly or indirectly involved in plant response to pathogen infection. In leaves, in contrast to results observed in roots, stresses impact carotenoid content depending on the genotype and the year. Moreover, carotenoid content variations were correlated to chlorophyll contents suggesting that a common mechanism of regulation for photosynthetic biosynthesis pigment exists