QTL × genetic background interaction: predicting inbred progeny value     

Jean-Luc Jannink 《Euphytica》2008,161(1-2):61-69

Failures of the additive infinitesimal model continue to provide incentive to study other modes of gene action, in particular, epistasis. Epistasis can be modeled as a QTL by genetic background interaction. Association mapping models lend themselves to fitting such an interaction because they often include both main marker and genetic background factors. In this study, I review a model that fits the QTL by background interaction as an added random effect in the now standard mixed model framework of association analyses. The model is applied to four-generation pedigrees where the objective is to predict the genotypic values of fourth-generation individuals that have not been phenotyped. In particular, I look at how well epistatic effects are estimated under two levels of inbreeding. Interaction detection power was 8% and 65% for pedigrees of 240 randomly mated individuals when the interaction generated 6% and 20% of the phenotypic variance, respectively. Power increased to 21% and 94% for these conditions when evaluated individuals were inbred by selfing four times. The interaction variance was estimated in an unbiased way under both levels of inbreeding, but its mean squared error was reduced by 40% to 70% when estimated in inbred relative to randomly mated individuals. The performance of the epistatic model was also enhanced relative to the additive model by inbreeding. These results are promising for the application of the model to typically self-pollinating crops such as wheat and soybean. The U.S. Government's right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.  相似文献   

Use the insiders: could insect facultative symbionts control vector-borne plant diseases?     

Julien Chuche  Nathalie Auricau-Bouvery  Jean-Luc Danet  Denis Thiéry 《Journal of pest science》2017,90(1):51-68

Insect vector-borne plant diseases, particularly those whose causative agents are viral, or phloem- and xylem-restricted bacteria, greatly impact crop losses. Since plants are immobile, the epidemiology of vector-borne diseases greatly depends on insect vectors, which are the only means of dissemination for many pathogens. The effectiveness of a vector-borne pathogen relies upon the vectorial capacity, which is affected by vector density, feeding activity on hosts, longevity before and after pathogen ingestion, duration of the incubation period, and vector competence. During the last decade, research on human vector-borne epidemics has stimulated interest in novel control strategies targeting different parts of the vector cycle, and our purpose here is to draw parallels between this field of research and agronomy. We review the literature on insect vectors of crop diseases and their symbiotic microorganisms with the aim of suggesting future integrated management techniques based on current research on insect-vectored human diseases. Vector transmission is a complex process and different modes of transmission are encountered irrespective of the pathogen. Facultative symbionts have varied effects on life history traits that could be used for vector population control. Symbiont selection, transformation, and their manner of dissemination are important when developing an integrated vector management system based on symbiont manipulation. In the short term, progress on our knowledge of the microflora of insect vectors of plant diseases must be made. In the long term, symbiont manipulation, which has been successfully demonstrated against human insect-vectored diseases, could be adapted to insect-borne plant diseases to increase sustainable crop production.  相似文献   

Antimicrobial Compounds from Eukaryotic Microalgae against Human Pathogens and Diseases in Aquaculture     

Charlotte Falaise  Cyrille Fran?ois  Marie-Agnès Travers  Benjamin Morga  Jo?l Haure  Réjean Tremblay  Fran?ois Turcotte  Pamela Pasetto  Romain Gastineau  Yann Hardivillier  Vincent Leignel  Jean-Luc Mouget 《Marine drugs》2016,14(9)

The search for novel compounds of marine origin has increased in the last decades for their application in various areas such as pharmaceutical, human or animal nutrition, cosmetics or bioenergy. In this context of blue technology development, microalgae are of particular interest due to their immense biodiversity and their relatively simple growth needs. In this review, we discuss about the promising use of microalgae and microalgal compounds as sources of natural antibiotics against human pathogens but also about their potential to limit microbial infections in aquaculture. An alternative to conventional antibiotics is needed as the microbial resistance to these drugs is increasing in humans and animals. Furthermore, using natural antibiotics for livestock could meet the consumer demand to avoid chemicals in food, would support a sustainable aquaculture and present the advantage of being environmentally friendly. Using natural and renewable microalgal compounds is still in its early days, but considering the important research development and rapid improvement in culture, extraction and purification processes, the valorization of microalgae will surely extend in the future.  相似文献   

‘<Emphasis Type="Italic">Candidatus</Emphasis> Phlomobacter fragariae’ and the proteobacterium associated with the low sugar content syndrome of sugar beet are related to bacteria of the arsenophonus clade detected in hemipteran insects     

Pascal Salar  Olivier Sémétey  Jean-Luc Danet  Elisabeth Boudon-Padieu  Xavier Foissac 《European journal of plant pathology / European Foundation for Plant Pathology》2010,126(1):123-127

The phylogeny of ‘Candidatus Phlomobacter fragariae’(Ca. P. fragariae), the agent of the strawberry marginal chlorosis (SMC), and the proteobacterium associated with the low sugar content syndrome of sugar beet (SBRp) is not well understood. The spoT-spoU-recG genetic locus initially characterised by genome walking from a ‘Ca. P. fragariae’ partial spoT sequence was used to determine relatedness of ‘Ca. P. fragariae’ and SBRp with bacteria detected in hemipteran insects. Both plant pathogenic bacteria belong to the same phylogenetic group as bacteria of the arsenophonus clade detected in hemipteran insects. The SBRp is closely related to arsenophonus-like proteobacteria from cixiids and more distantly related to psyllid and delphacid secondary endosymbionts, whereas the relatives of ‘Ca. P. fragariae’ remain to be discovered. No genetic variability was found among isolates of ‘Ca. P. fragariae’ or SBRp. Implications for explaining the emergence of both ‘Ca. P. fragariae’ and SBRp as epidemic plant pathogens are discussed.  相似文献   

SWORM: an agent-based model to simulate the effect of earthworms on soil structure     

E. Blanchart    N. Marilleau    J.-L. Chotte    A. Drogoul    E. Perrier  & Ch. Cambier 《European Journal of Soil Science》2009,60(1):13-21

Soil structure can be defined as the spatial organization of solid mineral and organic particles, and pore space. It is of great importance for soil functioning as it drives ecosystem functions (carbon sequestration, emission of greenhouse gases, nutrient cycling, primary productivity, etc.). Soil structure results from biotic and abiotic factors. Among biotic factors, numerous studies have shown the importance of organic matter, microorganisms, roots and invertebrates. Earthworms are known to play a key role in soil structure formation and maintenance through a continuous production of biogenic structures (casts and burrows). As far as we know, no models describe or quantify the effect of soil invertebrates on soil aggregation and porosity. It is a challenge to describe the physical soil environment for purposes of modelling because a soil is a multi‐scale heterogeneous, three‐dimensional and dynamic environment. An approach based on fractal theory (often used in soil sciences) was chosen to model such a real complex environment; it was integrated into a multi‐agent system (MAS), which allows us to simulate agents (e.g. earthworms) situated in a virtual world (e.g. soil). It is a bottom‐up approach that allows us to describe a system at a micro level (e.g. earthworms and their local soil environment) in order to observe, during simulations, macroscopic changes (e.g. soil structure evolution, organic matter dynamics, and microbial functions). In this paper we describe the SWORM (for ‘Simulated Worms’) model and the simulator, and present the results of the simulation applied to a case study. The effect of compacting and decompacting earthworm species on the structure of humid savanna soil at Lamto in Côte d’Ivoire has been widely studied. Quantitative and graphical outputs (e.g. thin sections of the virtual soil) indicate that the simulator was able to reproduce the effects of both compacting and decompacting species. Different ways to improve the model are discussed.  相似文献   

The search for biologically active secondary metabolites     

Kurt Hostettmann  Jean-Luc Wolfender 《Pest management science》1997,51(4):471-482

Plants provide a rich source of novel biologically active compounds. Biological and chemical screenings are complementary approaches for the rapid detection and isolation of interesting new plant constituents. Biological screening followed by activity-guided fractionation has been used successfully in our laboratories for the discovery of antifungal, larvicidal and molluscicidal compounds. High performance liquid chromatography (HPLC) coupled to UV spectroscopy (LC/UV), mass spectrometry (LC/MS) and nuclear magnetic resonance (LC/NMR) has proved to be highly efficient for the chemical screening of crude plant extracts. In particular LC/MS and LC/MS/MS used with different ionisation techniques such as thermospray (TSP), continuous flow-FAB (CF-FAB) and electrospray (ES) have proved to be very efficient for the early recognition of molluscicidal saponins in Swartzia madagascariensis and Phytolacca dodecandra. The combination of LC/UV/NMR/MS was of great value for the investigation of polyphenols and bitter principles in Gentianaceae species. Among other examples, LC/NMR analysis of the antifungal crude extract of the African plant Swertia calycina is presented. ©1997 SCI  相似文献   

Effects of cropping systems,maize residues application and N fertilization on promiscuous soybean yields and diversity of native rhizobia in Central Kenya     

L. Herrmann  J.L. Chotte  M. Thuita  D. Lesueur 《Pedobiologia》2014

Agriculture intensification has resulted in severe soil nutrient depletion in Africa. Alternative agricultural practices have been promoted to reduce the use of expensive mineral fertilizers and to restore and sustain soil fertility. The use of mineral fertilizer combined with organic inputs (such as crop residues) and different cropping systems (cereal–legume association or rotation) have been particularly promising. Impacts of these agricultural practices on soil communities have been widely studied, yet little is known on the effect on more specific groups such as rhizobia. A field trial was set up in Chuka (Kenya) to assess the impact of different cropping systems (maize and soybean in intercropping, rotation or monocropping) combined with N fertilization and residues application on the genetic diversity of promiscuous soybean rhizobia during two seasons. Soybean yields were severely reduced by moisture stress and the association with maize compared to mono-legume and rotation systems. Nodulation was generally low but was positively affected by residues application. Diversity of native rhizobia was very low (Shannon indices H′ < 0.8) across the experiment and was not affected by the treatments. Only 5 IGS profiles were obtained after RFLP analysis and all isolated rhizobia were identified as Bradyrhizobium elkanii. The distribution of the different IGS groups within the experiment was more affected by season and residues application than by cropping system and nitrogen fertilizer application. These results suggest a limited population and a low diversity of indigenous rhizobia, and emphasize the need of alternative managements to increase and sustain soybean yields in Central Kenya.  相似文献   

Influence of abiotic factors,inoculum source,and cultivar susceptibility on the potato tuber blemish diseases black dot (Colletotrichum coccodes) and silver scurf (Helminthosporium solani)     

Josep Massana-Codina  Sylvain Schnee  Nicole Lecoultre  Eric Droz  Brice Dupuis  Andreas Keiser  Patrice de Werra  Jean-Luc Wolfender  Katia Gindro  Stéphanie Schürch 《Plant pathology》2021,70(4):885-897

Black dot and silver scurf are potato blemish diseases whose economic impact has increased in recent years. Because their symptomatology on tubers is visually similar, disease assessment does not usually differentiate between the two pathogens, which share the same ecological niche. The epidemiology of black dot has been extensively studied, especially in the UK, but the factors that influence silver scurf have been less investigated. In this study, the influence of cultivar, source of inoculum, and environmental conditions on both diseases was studied in field trials over a three-year period (2016–2018) in Switzerland. Planting minitubers did not prevent either disease in daughter tubers, indicating the contribution of soil as an inoculum reservoir. An arbitrary threshold of Colletotrichum coccodes soil inoculum could be set to discriminate between low and high disease risk. For the first time, Helminthosporium solani DNA was detected in stolons, and infections appeared earlier in stolons than in tubers. H. solani stolon and tuber infections usually appeared later in the season than those of C. coccodes. Black dot severity correlated positively with precipitation, while silver scurf severity correlated positively with temperature. Table potato cultivars commonly grown in Switzerland exhibited significant differences in susceptibility to both diseases, and cultivars with low susceptibility to both silver scurf and black dot were identified. These results gave new insights into understanding the factors driving the epidemiology of potato blemish diseases and may contribute to building a risk assessment scheme to manage both diseases simultaneously.  相似文献   

Diversity of avipoxviruses in captive-bred Houbara bustard     

Guillaume Le Loc’h  Mariette F Ducatez  Christelle Camus-Bouclainville  Jean-Luc Guérin  Stéphane Bertagnoli 《Veterinary research》2014,45(1)

Implementation of conservation breeding programs is a key step to ensuring the sustainability of many endangered species. Infectious diseases can be serious threats for the success of such initiatives especially since knowledge on pathogens affecting those species is usually scarce. Houbara bustard species (Chlamydotis undulata and Chlamydotis macqueenii), whose populations have declined over the last decades, have been captive-bred for conservation purposes for more than 15 years. Avipoxviruses are of the highest concern for these species in captivity. Pox lesions were collected from breeding projects in North Africa, the Middle East and Central Asia for 6 years in order to study the diversity of avipoxviruses responsible for clinical infections in Houbara bustard. Molecular and phylogenetic analyses of 113 and 75 DNA sequences for P4b and fpv140 loci respectively, revealed an unexpected wide diversity of viruses affecting Houbara bustard even at a project scale: 17 genotypes equally distributed between fowlpox virus-like and canarypox virus-like have been identified in the present study. This suggests multiple and repeated introductions of virus and questions host specificity and control strategy of avipoxviruses. We also show that the observed high virus burden and co-evolution of diverse avipoxvirus strains at endemic levels may be responsible for the emergence of novel recombinant strains.  相似文献   

Analytical discrimination of poisonous and nonpoisonous chemotypes of giant fennel (Ferula communis L.) through their biologically active and volatile fractions     

Rubiolo P  Matteodo M  Riccio G  Ballero M  Christen P  Fleury-Souverain S  Veuthey JL  Bicchi C 《Journal of agricultural and food chemistry》2006,54(20):7556-7563

Giant fennel (Ferula communis L.) from Sardinia is characterized by two chemotypes with different biological activities. One chemotype is poisonous, due to prenylcoumarins, and responsible for ferulosis, which mainly affects sheep and goats, cattle, and horses; the other chemotype is nonpoisonous and contains daucane esters. The two chemotypes cannot be distinguished botanically. High-performance liquid chromatography-diode array-ultraviolet detection-mass spectrometry (HPLC-DAD-UV-MS) analysis of the composition of the fractions containing the biologically active metabolites and of the volatile fractions, by gas chromatography-mass spectrometry (GC-MS), of both essential oil and headspace sampled by headspace solid-phase microextraction (HS-SPME) are here shown to be effective in discriminating the poisonous and nonpoisonous chemotypes. HS-SPME with CAR/PDMS/DVB in combination with GC-MS has also been found to be a successful, fully automated one-step method for rapid and unequivocal discrimination of the two chemotypes, using aristolene and allohedycaryol as markers of the poisonous and nonpoisonous chemotypes, respectively.  相似文献