Structuration de la diversité génétique chez la luzerne cultivée, conséquence pour l'identification de gènes liés à des caractères agronomiques

La luzerne, espèce allogame et autotétraploïde, est une légumineuse fourragère dont l’intérêt connaît un renouveau certain grâce à ses atouts pour le développement durable de l’agriculture. L’amélioration des variétés nécessite de mieux connaître les ressources génétiques, pour les exploiter, que ce soit en sélection classique ou en utilisant les outils moléculaires pour implémenter la sélection assistée par marqueurs. En étudiant 10 variétés européennes, nous avons montré que la diversité à l’intérieur des variétés est grande (hétérozygotie attendue de 0.75, déviation standard de 0.80, pour des caractères phénotypiques et des marqueurs moléculaires neutres, respectivement). La différenciation entre variétés est notable pour les caractères phénotypiques. Cette structuration de la diversité est favorable à l’utilisation de la génétique d’association basée sur des gènes candidats pour identifier des gènes liés à des caractères agronomiques. Une telle étude a permis de montrer que le gène Constans-like contribue à expliquer les différences de longueur de tiges chez la luzerne, une composante du rendement fourrager. Alfalfa, an allogamous and autotetraploid species, is a forage legume for which a renewed interest has raised because of its advantages for a sustainable agriculture. Variety improvement requires a better knowledge of the genetic resources in order to exploit them, with classical breeding methods or with molecular tools to implement marker assisted selection. We have described 10 European varieties and found a large within-variety diversity (expected heterozygozity of 0.75, standard deviation of 0.80, with phenotypic traits and neutral molecular markers, respectively). Differentiation between varieties was noticeable for phenotypic traits. This genetic structure of diversity is favourable to the use of association genetics based on candidate genes to identify genes related to agronomic traits. Such a study showed that Constans-like gene contributes to explain differences in alfalfa stem length, a component of forage yield

Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers

BACKGROUND: Alfalfa (Medicago sativa) is a major forage crop. The genetic progress is slow in this legume species because of its autotetraploidy and allogamy. The genetic structure of this species makes the construction of genetic maps difficult. To reach this objective, and to be able to detect QTLs in segregating populations, we used the available codominant microsatellite markers (SSRs), most of them identified in the model legume Medicago truncatula from EST database. A genetic map was constructed with AFLP and SSR markers using specific mapping procedures for autotetraploids. The tetrasomic inheritance was analysed in an alfalfa mapping population. RESULTS: We have demonstrated that 80% of primer pairs defined on each side of SSR motifs in M. truncatula EST database amplify with the alfalfa DNA. Using a F1 mapping population of 168 individuals produced from the cross of 2 heterozygous parental plants from Magali and Mercedes cultivars, we obtained 599 AFLP markers and 107 SSR loci. All but 3 SSR loci showed a clear tetrasomic inheritance. For most of the SSR loci, the double-reduction was not significant. For the other loci no specific genotypes were produced, so the significant double-reduction could arise from segregation distortion. For each parent, the genetic map contained 8 groups of four homologous chromosomes. The lengths of the maps were 2649 and 3045 cM, with an average distance of 7.6 and 9.0 cM between markers, for Magali and Mercedes parents, respectively. Using only the SSR markers, we built a composite map covering 709 cM. CONCLUSIONS: Compared to diploid alfalfa genetic maps, our maps cover about 88–100% of the genome and are close to saturation. The inheritance of the codominant markers (SSR) and the pattern of linkage repulsions between markers within each homology group are consistent with the hypothesis of a tetrasomic meiosis in alfalfa. Except for 2 out of 107 SSR markers, we found a similar order of markers on the chromosomes between the tetraploid alfalfa and M. truncatula genomes indicating a high level of colinearity between these two species. These maps will be a valuable tool for alfalfa breeding and are being used to locate QTLs

Association study between the gibberellic acid insensitive gene and leaf length in a Lolium perenne L. synthetic variety

<p>Abstract</p> <p>Background</p> <p>Association studies are of great interest to identify genes explaining trait variation since they deal with more than just a few alleles like classical QTL analyses. They are usually performed using collections representing a wide range of variability but which could present a genetic substructure. The aim of this paper is to demonstrate that association studies can be performed using synthetic varieties obtained after several panmictic generations. This demonstration is based on an example of association between the gibberellic acid insensitive gene (GAI) polymorphism and leaf length polymorphism in 'Herbie', a synthetic variety of perennial ryegrass.</p> <p>Methods</p> <p>Leaf growth parameters, consisted of leaf length, maximum leaf elongation rate (LERmax) and leaf elongation duration (LED), were evaluated in spring and autumn on 216 plants of Herbie with three replicates. For each plant, a sequence of 370 bp in GAI was analysed for polymorphism.</p> <p>Results</p> <p>Genetic effect was highly significant for all traits. Broad sense heritabilities were higher for leaf length and LERmax with about 0.7 in each period and 0.5 considering both periods than for LED with about 0.4 in each period and 0.3 considering both periods. GAI was highly polymorphic with an average of 12 bp between two consecutive SNPs and 39 haplotypes in which 9 were more frequent. Linkage disequilibrium declined rapidly with distance with r ²values lower than 0.2 beyond 150 bp. Sequence polymorphism of GAI explained 8-14% of leaf growth parameter variation. A single SNP explained 4% of the phenotypic variance of leaf length in both periods which represents a difference of 33 mm on an average of 300 mm.</p> <p>Conclusions</p> <p>Synthetic varieties in which linkage disequilibrium declines rapidly with distance are suitable for association studies using the "candidate gene" approach. GAI polymorphism was found to be associated with leaf length polymorphism which was more correlated to LERmax than to LED in Herbie. It is a good candidate to explain leaf length variation in other plant material.</p

Developing a French FrameNet: Methodology and First results

International audienceThe Asfalda project aims to develop a French corpus with frame-based semantic annotations and automatic tools for shallow semantic analysis. We present the first part of the project: focusing on a set of notional domains, we delimited a subset of English frames, adapted them to French data when necessary, and developed the corresponding French lexicon. We believe that working domain by domain helped us to enforce the coherence of the resulting resource, and also has the advantage that, though the number of frames is limited (around a hundred), we obtain full coverage within a given domain

Foisonnement de l'innovation agricole : quelques exemples d'initiatives en élevage herbivore

Les témoignages rassemblés pour illustrer le foisonnement des innovations agricoles émanent d'acteurs différents (agriculteurs, recherche, développement) mais sont tous caractérisés par des approches plutôt systémiques et des dynamiques de co-conception. Les thèmes abordés concernent la production (valorisation des surfaces avec des cultures dérobées, sélection d'espèce prairiales locales), l'appropriation de résultats de recherche (amélioration de la gestion des prairies), la conception d'itinéraires techniques (solutions pour limiter les pertes d'azote en rotation prairie - prairie), l'évaluation de systèmes (repérer des pratiques innovantes en mobilisant des principes de l'agroécologie) mais aussi l'amélioration des conditions de travail et la formation (communication « intergénérationnelle » entre des paysans herbagers et des élèves)

Developing a Sustainable and Circular Bio-Based Economy in EU:By Partnering Across Sectors, Upscaling and Using New Knowledge Faster, and For the Benefit of Climate, Environment &amp; Biodiversity, and People &amp; Business

This paper gives an overview of development of the EU-bioeconomy, 2014-2020. The Vision of the new Circular Bio-based Economy, CBE is presented: Unlocking the full potential of all types of sustainably sourced biomass, crop residues, industrial side-streams, and wastes by transforming it into value-added products. The resulting product portfolio consists of a wide spectrum of value-added products, addressing societal and consumer needs. Food and feed, bio-based chemicals, materials, healthpromoting products; and bio-based fuels. The pillars of CBE are described, including biotechnology, microbial production, enzyme technology, green chemistry, integrated physical/chemical processing, policies, conducive framework conditions and public private partnerships. Drivers of CBE are analyzed: Biomass supply, biorefineries, value chain clusters, rural development, farmers, foresters and mariners; urgent need for climate change mitigation and adaptation, and stopping biodiversity loss. Improved framework conditions can be drivers but also obstacles if not updated to the era of circularity. Key figures, across the entire BBI-JU project portfolio (20142020) are provided, including expansion into biomass feedstocks, terrestrial and aquatic, and an impressive broadening of bio-based product portfolio, including higher-value, healthpromoting products for man, animal, plants and soil. Parallel to this, diversification of industrial segments and types of funding instruments developed, reflecting industrial needs and academic research involvement. Impact assessment is highlighted. A number of specific recommendations are given; e.g., including international win/win CBEcollaborations, as e.g., expanding African EU collaboration into CBE. In contrast to fossil resources biological resources are found worldwide. In its outset, circular biobased economy, can be implemented all over, in a just manner, not the least stimulating rural developmentThis study received funding only for covering the production costs (carried by the public BBI-JU secretariat).info:eu-repo/semantics/publishedVersio

Patient selection for laparoscopic excision of adrenal metastases: a multicenter cohort study

International audienceIntroduction The use of laparoscopy for the excision of adrenal metastasis remains controversial. We aimed to report oncological and perioperative outcomes of laparoscopic excision of adrenal metastases and to seek for predictive factors of unfavourable oncological outcomes. Methods A retrospective chart review was conducted and all consecutive patients who underwent laparoscopic adrenalectomy (LA) in the setting of metastatic cancer in two academic urology departments from November 2006 through January 2014 were included. Primary tumors were categorized as pulmonary, renal or “other primary” tumors to allow statistical comparison. Unfavourable surgical outcomes were defined as the occurrence of either postoperative complications and/or positive surgical margins. Results Forty-three patients who underwent a total of 45 LA were included for analysis. There were 8 complications (17.8%). Positive surgical margins were found in 12 specimens (26.7%). After a median follow-up of 37 months, estimated overall survival rates were 89.5% and 51.5% at 1 year and 5 years, respectively. In multivariable analysis the only predictor of unfavourable surgical outcomes was a tumor size &gt; 5 cm (OR= 20.5; p=0.001). In multivariate analysis the pulmonary (OR=0.3; p=0.008) or “other” (OR= 0.1; p=0.0006) origin of the primary tumor was the only prognostic factor of shorter cancer specific survival. Conclusion Laparoscopic resection of adrenal metastasis can be safely performed in most patients but is associated with an increased risk of positive surgical margins and postoperative complications in larger tumors (&gt;5 cm). Adrenalectomy provides better oncological outcomes in metastases from renal cell carcinoma compared to other primary tumors

Transancestral fine-mapping of four type 2 diabetes susceptibility loci highlights potential causal regulatory mechanisms.

To gain insight into potential regulatory mechanisms through which the effects of variants at four established type 2 diabetes (T2D) susceptibility loci (CDKAL1, CDKN2A-B, IGF2BP2 and KCNQ1) are mediated, we undertook transancestral fine-mapping in 22 086 cases and 42 539 controls of East Asian, European, South Asian, African American and Mexican American descent. Through high-density imputation and conditional analyses, we identified seven distinct association signals at these four loci, each with allelic effects on T2D susceptibility that were homogenous across ancestry groups. By leveraging differences in the structure of linkage disequilibrium between diverse populations, and increased sample size, we localised the variants most likely to drive each distinct association signal. We demonstrated that integration of these genetic fine-mapping data with genomic annotation can highlight potential causal regulatory elements in T2D-relevant tissues. These analyses provide insight into the mechanisms through which T2D association signals are mediated, and suggest future routes to understanding the biology of specific disease susceptibility loci

Trans-ancestry meta-analyses identify rare and common variants associated with blood pressure and hypertension

High blood pressure is a major risk factor for cardiovascular disease and premature death. However, there is limited knowledge on specific causal genes and pathways. To better understand the genetics of blood pressure, we genotyped 242,296 rare, low-frequency and common genetic variants in up to ~192,000 individuals, and used ~155,063 samples for independent replication. We identified 31 novel blood pressure or hypertension associated genetic regions in the general population, including three rare missense variants in RBM47, COL21A1 and RRAS with larger effects (>1.5mmHg/allele) than common variants. Multiple rare, nonsense and missense variant associations were found in A2ML1 and a low-frequency nonsense variant in ENPEP was identified. Our data extend the spectrum of allelic variation underlying blood pressure traits and hypertension, provide new insights into the pathophysiology of hypertension and indicate new targets for clinical intervention

The genetic architecture of type 2 diabetes

The genetic architecture of common traits, including the number, frequency, and effect sizes of inherited variants that contribute to individual risk, has been long debated. Genome-wide association studies have identified scores of common variants associated with type 2 diabetes, but in aggregate, these explain only a fraction of heritability. To test the hypothesis that lower-frequency variants explain much of the remainder, the GoT2D and T2D-GENES consortia performed whole genome sequencing in 2,657 Europeans with and without diabetes, and exome sequencing in a total of 12,940 subjects from five ancestral groups. To increase statistical power, we expanded sample size via genotyping and imputation in a further 111,548 subjects. Variants associated with type 2 diabetes after sequencing were overwhelmingly common and most fell within regions previously identified by genome-wide association studies. Comprehensive enumeration of sequence variation is necessary to identify functional alleles that provide important clues to disease pathophysiology, but large-scale sequencing does not support a major role for lower-frequency variants in predisposition to type 2 diabetes