Identifying QTLs involved in hybrid performance and heterotic group complementarity: new GWAS models applied to factorial and admixed diallel maize hybrid panels.

An original GWAS model integrating the ancestry of alleles was proposed and allowed the detection of background specific additive and dominance QTLs involved in heterotic group complementarity and hybrid performance. Maize genetic diversity is structured into genetic groups selected and improved relative to each other. This process increases group complementarity and differentiation over time and ensures that the hybrids produced from inter-group crosses exhibit high performances and heterosis.

Improving genomic predictions with inbreeding and nonadditive effects in two admixed maize hybrid populations in single and multienvironment contexts.

Genetic admixture, resulting from the recombination between structural groups, is frequently encountered in breeding populations. In hybrid breeding, crossing admixed lines can generate substantial nonadditive genetic variance and contrasted levels of inbreeding which can impact trait variation. This study aimed at testing recent methodological developments for the modeling of inbreeding and nonadditive effects in order to increase prediction accuracy in admixed populations.

The Pitfalls of Heterosis Coefficients.

Heterosis (hybrid vigour) is a universal phenomenon of crucial agro-economic and evolutionary importance. We show that the most common heterosis coefficients do not properly measure deviation from additivity because they include both a component accounting for "real" heterosis and a term that is not related to heterosis, since it is derived solely from parental values. Therefore, these coefficients are inadequate whenever the aim of the study is to compare heterosis levels between different traits, environments, genetic backgrounds, or developmental stages, as these factors may affect not only the level of non-additivity, but also parental values.

Heterosis Is a Systemic Property Emerging From Non-linear Genotype-Phenotype Relationships: Evidence From Genetics and Computer Simulations.

Heterosis, the superiority of hybrids over their parents for quantitative traits, represents a crucial issue in plant and animal breeding as well as evolutionary biology. Heterosis has given rise to countless genetic, genomic and molecular studies, but has rarely been investigated from the point of view of systems biology. We hypothesized that heterosis is an emergent property of living systems resulting from frequent concave relationships between genotypic variables and phenotypes, or between different phenotypic levels.

Influence of water temperature and food on the last stages of cultured pearl mineralization from the black-lip pearl oyster Pinctada margaritifera.

Environmental parameters, such as food level and water temperature, have been shown to be major factors influencing pearl oyster shell growth and molecular mechanisms involved in this biomineralization process. The present study investigates the effect of food level (i.e.

Uranium perturbs signaling and iron uptake response in Arabidopsis thaliana roots.

Uranium is a natural element which is mainly redistributed in the environment due to human activity, including accidents and spillages. Plants may be useful in cleaning up after incidents, although little is yet known about the relationship between metal speciation and plant response. Here, J-Chess modeling was used to predict U speciation and exposure conditions affecting U bioavailability for plants.

Functional divergence in shrimp anti-lipopolysaccharide factors (ALFs): from recognition of cell wall components to antimicrobial activity.

Antilipopolysaccharide factors (ALFs) have been described as highly cationic polypeptides with a broad spectrum of potent antimicrobial activities. In addition, ALFs have been shown to recognize LPS, a major component of the Gram-negative bacteria cell wall, through conserved amino acid residues exposed in the four-stranded β-sheet of their three dimensional structure. In penaeid shrimp, ALFs form a diverse family of antimicrobial peptides composed by three main variants, classified as ALF Groups A to C.

Big defensins, a diverse family of antimicrobial peptides that follows different patterns of expression in hemocytes of the oyster Crassostrea gigas.

Background: Big defensin is an antimicrobial peptide composed of a highly hydrophobic N-terminal region and a cationic C-terminal region containing six cysteine residues involved in three internal disulfide bridges. While big defensin sequences have been reported in various mollusk species, few studies have been devoted to their sequence diversity, gene organization and their expression in response to microbial infections.

Findings: Using the high-throughput Digital Gene Expression approach, we have identified in Crassostrea gigas oysters several sequences coding for big defensins induced in response to a Vibrio infection.

Systemic properties of metabolic networks lead to an epistasis-based model for heterosis.

The genetic and molecular approaches to heterosis usually do not rely on any model of the genotype-phenotype relationship. From the generalization of Kacser and Burns' biochemical model for dominance and epistasis to networks with several variable enzymes, we hypothesized that metabolic heterosis could be observed because the response of the flux towards enzyme activities and/or concentrations follows a multi-dimensional hyperbolic-like relationship. To corroborate this, we used the values of systemic parameters accounting for the kinetic behaviour of four enzymes of the upstream part of glycolysis, and simulated genetic variability by varying in silico enzyme concentrations.

Oyster hemocytes express a proline-rich peptide displaying synergistic antimicrobial activity with a defensin.

A cDNA sequence that encodes a 61-amino acid polypeptide precursor with homologies to proline-rich antimicrobial peptides (AMPs) was identified in the oyster Crassostrea gigas. After release of a hydrophobic signal peptide, the resulting 37-amino acid peptide, Cg-Prp, is composed of an acidic region and a cationic proline-rich region. To evaluate the biological properties of Cg-Prp, multiple proline-rich peptides corresponding to putative processing of the full-length Cg-Prp were synthesized.

A relationship between antimicrobial peptide gene expression and capacity of a selected shrimp line to survive a Vibrio infection.

Understanding of antimicrobial defence mechanisms of penaeid shrimp should help in the design of efficient strategies for the management and disease control in aquaculture. In this study, we have specifically analysed the expression in circulating hemocytes of antimicrobial peptides (AMPs) encoding genes, such as PEN2 and PEN3, ALF, crustin, lysozyme and a putative cysteine-rich peptide. We evidenced a relationship between the level of expression of some AMPs and the successful response of the shrimp, Litopenaeus stylirostris, to circumvent a pathogenic Vibrio penaeicida infection.

Evidence of a bactericidal permeability increasing protein in an invertebrate, the Crassostrea gigas Cg-BPI.

A cDNA sequence with homologies to members of the LPS-binding protein and bactericidal/permeability-increasing protein (BPI) family was identified in the oyster Crassostrea gigas. The recombinant protein was found to bind LPS, to display bactericidal activity against Escherichia coli, and to increase the permeability of the bacterial cytoplasmic membrane. This indicated that it is a BPI rather than an LPS-binding protein.

Localization of deformed wing virus infection in queen and drone Apis mellifera L.

The distribution of deformed wing virus infection within the honey bee reproductive castes (queens, drones) was investigated by in situ hybridization and immunohistology from paraffin embedded sections. Digoxygenin or CY5.5 fluorochrome end-labelled nucleotide probes hybridizing to the 3' portion of the DWV genome were used to identify DWV RNA, while a monospecific antibody to the DWV-VP1 structural protein was used to identify viral proteins and particles.

The early responses of Arabidopsis thaliana cells to cadmium exposure explored by protein and metabolite profiling analyses.

To get more insight into plant cell response to cadmium (Cd) stress, both proteomic and metabolomic "differential display" analyses were performed on Arabidopsis thaliana cells exposed to different concentrations of the toxic chemical. After a 24 h treatment, soluble proteins extracted from untreated and treated cells were separated by 2-D-PAGE and image analyses were performed to quantify and compare protein levels. Proteins up- and down-regulated in response to Cd were identified by MS and mapped into specific metabolic pathways and cellular processes, highlighting probable activation of the carbon, nitrogen, and sulfur metabolic pathways.

Simplified modelling of metabolic pathways for flux prediction and optimization: lessons from an in vitro reconstruction of the upper part of glycolysis.

Explicit modelling of metabolic networks relies on well-known mathematical tools and specialized computer programs. However, identifying and estimating the values of the very numerous enzyme parameters inherent to the models remain a tedious and difficult task, and the rate equations of the reactions are usually not known in sufficient detail. A way to circumvent this problem is to use 'non-mechanistic' models, which may account for the behaviour of the systems with a limited number of parameters.

Characterization of a defensin from the oyster Crassostrea gigas. Recombinant production, folding, solution structure, antimicrobial activities, and gene expression.

In invertebrates, defensins were found in arthropods and in the mussels. Here, we report for the first time the identification and characterization of a defensin (Cg-Def) from an oyster. Cg-def mRNA was isolated from Crassostrea gigas mantle using an expressed sequence tag approach.

An extension to the metabolic control theory taking into account correlations between enzyme concentrations.

The classical metabolic control theory [Kacser, H. & Burns, J.A.

Assessing factors for reliable quantitative proteomics based on two-dimensional gel electrophoresis.

We statistically analysed various factors to get accurate estimates of protein quantities from two-dimensional gels. Yeast proteins were labelled with (35)S or stained with Coomassie Brilliant Blue G-250, and spots were automatically quantified with software packages Kepler, ImageQuaNT, Melanie 3.0 and Progenesis.

A new class (penaeidin class 4) of antimicrobial peptides from the Atlantic white shrimp (Litopenaeus setiferus) exhibits target specificity and an independent proline-rich-domain function.

A highly pure, chemically defined representative of a new class of antimicrobial peptide from the Atlantic white shrimp (Litopenaeus setiferus), penaeidin class 4 [Pen4-1 (penaeidin class 4 isoform 1)], was produced synthetically. Chemical synthesis was achieved by native ligation from two separate domains yielding a bioactive peptide that reflected the characteristics of native penaeidin. Synthetic Pen4-1 proved to be an effective antimicrobial peptide, particularly against the broad-spectrum pathogen Fusarium oxysporum, exhibiting a complex effect on reproductive growth at inhibitory concentrations resulting in the suppression of spore formation.