Historique de l'amélioration de la canne à sucre et état de l'art des recherches en génétique d'association pour le rendement

La sélection de la canne à sucre est récente, elle commence lors de la création des premiers hybrides obtenus à Java au début du siècle dernier. La nobilisation, une méthode de croisements interspécifiques, permit l'obtention de variétés nettement plus performantes et résistantes aux principaux pathogènes de la canne. Depuis, les centres croisent des variétés élites et la sélection se fait à partir du phénotypage des descendances. Utiliser l'information moléculaire pour la sélection d'élites serait une réelle avancée pour le sélectionneur. Bien que de nombreuses études en génétique d'association soient réalisées, aucun marqueur n'est aujourd'hui utilisé dans les schémas de sélection de la canne à sucre. Les effets des marqueurs ne sont pas estimés de façon assez précise et doivent être validés dans des populations indépendantes. L'association marqueurs-caractères est aujourd'hui complétée par de nouvelles approches telles que la sélection génomique et l'utilisation des modèles écophysiologiques dans la prédiction du rendement. (Résumé d'auteur

Streaming Binary Sketching based on Subspace Tracking and Diagonal Uniformization

In this paper, we address the problem of learning compact similarity-preserving embeddings for massive high-dimensional streams of data in order to perform efficient similarity search. We present a new online method for computing binary compressed representations -sketches- of high-dimensional real feature vectors. Given an expected code length $c$ and high-dimensional input data points, our algorithm provides a $c$-bits binary code for preserving the distance between the points from the original high-dimensional space. Our algorithm does not require neither the storage of the whole dataset nor a chunk, thus it is fully adaptable to the streaming setting. It also provides low time complexity and convergence guarantees. We demonstrate the quality of our binary sketches through experiments on real data for the nearest neighbors search task in the online setting

Macroion adsorption: The crucial role of excluded volume and coions

The adsorption of charged colloids (macroions) onto an oppositely charged planar substrate is investigated theoretically. Taking properly into account the finite size of the macroions, unusual behaviors are reported. It is found that the role of the coions (the little salt-ions carrying the same sign of charge as that of the substrate) is crucial to understand the mechanisms involved in the process of macroion adsorption. In particular, the coions can accumulate near the substrate's surface and lead to a counter-intuitive {\it surface charge amplification}.Comment: 11 pages - 4 figures. To appear in JC

Experimental validation of genomic selection in Sugarcane : P0197

Sugarcane cultivars (Saccharum spp.) are interspecific hybrids characterized by highly heterozygous and polyploid genome. Genomic selection (GS) approach is believed to be well suited for complex traits by including all markers in prediction models. Our objective was to test the GS approach in a complex polyploid crop. Predictions of genetic values were carried out on two independent panels, each composed of 167 cultivars and breeding materials covering the worldwide diversity. Accessions were genotyped using 1499 DArT. Phenotyping was carried out in Reunion for one panel and in Guadeloupe for the other one. We considered ten traits relative to sugar and fiber contents, digestibility and composition of the bagasse, plant morphology and disease resistances. We used seven predictive models: Bayesian Regression, Bayesian LASSO, Ridge-regression, BayesA, BayesB, Reproducing Kernel Hilbert Space and Partial Least Square Regression. Accuracies of predictions were assessed through correlations between observed and predicted genetic values, firstly by using a cross-validation within each panel, and secondly by using a cross-validation between panels. Accuracies of predictions were of similar value between the seven GS models for a given trait, while differences were observed among traits. Depending on the trait considered, the average GS accuracy values related to within-panel prediction ranged from 0.29 to 0.61 in the Reunion panel and from 0.13 to 0.5 in the Guadeloupe panel. GS accuracy values based on cross-validations between the two independent panels ranged from 0.13 (smut resistance) to 0.55 (brix). This study represents the first validation of GS approach in sugarcane with experimental data. (Résumé d'auteur

Ion condensation on charged patterned surfaces

We study ion condensation onto a patterned surface of alternating charges. The competition between self-energy and ion-surface interactions leads to the formation of ionic crystalline structures at low temperatures. We consider different arrangements of underlying ionic crystals, including single ion adsorption, as well as the formation of dipoles at the interface between charged domains. Molecular dynamic simulation illustrates existence of single and mixed phases. Our results contribute to understanding pattern recognition, and molecular separation and synthesis near patterned surfaces.Comment: 3 figure

Forcing reversibility in the no strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons

Because of the base pairing rules in DNA, some mutations experienced by a portion of DNA during its evolution result in the same substitution, as we can only observe differences in coupled nucleotides. Then, in the absence of a bias between the two DNA strands, a model with at most 6 different parameters instead of 12 is sufficient to study the evolutionary relationship between homologous sequences derived from a common ancestor. On the other hand the same symmetry reduces the number of independent observations which can be made. Such a reduction can in some cases invalidate the calculation of the parameters. A compromise between biologically acceptable hypotheses and tractability is introduced and a five parameter reversible no-strand-bias condition (RNSB) is presented. The identifiability of the parameters under this model is shown by examples.Comment: 12 pages, 4 figures, corrected typo

Independent Evaluation of the Water and Sanitation Hibah Program Indonesia

This evaluation assess the effectiveness of Indonesia's Water and Sanitation Hibah Program pilot and identifies lessons for applying this mechanism more broadly. The program, which operates by paying an agreed amount for verified household water or sanitation service connections installed by local water and sanitation utilities, takes advantage of excess capacity of water companies to bypass the need for infrastructure investment. It was evaluated through a document review, key informant interviews, a key stakeholder workshop, field work, and a beneficiary survey, along with quantitative data from existing sources

Nonlinear screening of charged macromolecules

We present several aspects of the screening of charged macromolecules in an electrolyte. After a review of the basic mean field approach, based on the linear Debye-Huckel theory, we consider the case of highly charged macromolecules, where the linear approximation breaks down and the system is described by full nonlinear Poisson-Boltzmann equation. Some analytical results for this nonlinear equation give some interesting insight on physical phenomena like the charge renormalization and the Manning counterion condensation