Searching for interacting QTL in related populations of an outbreeding species

Many important crop species are outbreeding. In outbreeding species the search for genes affecting traits is complicated by the fact that in a single cross up to four alleles may be present at each locus. This paper is concerned with the search for interacting quantitative trait loci (QTL) in populations which have been obtained by crossing a number of parents. It will be assumed that the parents are unrelated, but the methods can be extended easily to allow a pedigree structure. The approach has two goals: (1) finding QTL that are interacting with other loci and also loci which behave additively; (2) finding parents which segregate at two or more interacting QTL. Large populations obtained by crossing these parents can be used to study interactions in detail. QTL analysis is carried out by means of regression on predictions of QTL genotypes

Testing the membrane paradigm with holography

One version of the membrane paradigm states that as far as outside observers are concerned, black holes can be replaced by a dissipative membrane with simple physical properties located at the stretched horizon. We demonstrate that such a membrane paradigm is incomplete in several aspects. We argue that it generically fails to capture the massive quasinormal modes, unless we replace the stretched horizon by the exact event horizon, and illustrate this with a scalar field in a BTZ black hole background. We also consider as a concrete example linearized metric perturbations of a five-dimensional AdS-Schwarzschild black brane and show that a spurious excitation appears in the long-wavelength response that is only removed from the spectrum when the membrane paradigm is replaced by ingoing boundary conditions at the event horizon. We interpret this excitation in terms of an additional Goldstone boson that appears due to symmetry breaking by the classical solution ending on the stretched horizon rather than the event horizon.Comment: 5 pages, 1 figure; v2: improved presentation, typos fixed, figure fixed, conclusions unchanged; v3: further improvements in the presentation, conclusions unchanged; v4: shortened, published versio

Towards a holographic realization of the quarkyonic phase

Large-Nc QCD matter at intermediate baryon density and low temperatures has been conjectured to be in the so-called quarkyonic phase, i.e., to have a quark Fermi surface and on top of it a confined spectrum of excitations. It has been suggested that the presence of the quark Fermi surface leads to a homogeneous phase with restored chiral symmetry, which is unstable towards creating condensates that break both the chiral and translational symmetry. Motivated by these exotic features, we investigate properties of cold baryonic matter in the single-flavor Sakai-Sugimoto model, searching for a holographic realization of the quarkyonic phase. We use a simplified mean-field description and focus on the regime of parametrically large baryon densities, of the order of the square of the ’t Hooft coupling, as they turn out to lead to new physical effects similar to the ones occurring in the quarkyonic phase. One effect—the appearance of a particular marginally stable mode breaking translational invariance and linked with the presence of the Chern-Simons term in the flavor-brane Lagrangian—is known to occur in the deconfined phase of the Sakai-Sugimoto model, but turns out to be absent here. The other, completely new phenomenon that we, preliminarily, study using strong simplifying assumptions are density-enhanced interactions of the flavor-brane gauge field with holographically represented baryons. These seem to significantly affect the spectrum of vector and axial mesons and might lead to approximate chiral symmetry restoration in the lowest part of the spectrum, where the mesons start to qualitatively behave like collective excitations of the dense baryonic medium. We discuss the relevance of these effects for holographic searches of the quarkyonic phase and conclude with a discussion of various subtleties involved in constructing a mean-field holographic description of a dense baryonic medium

Co-production of high-protein feed and bio-oil for poultry protein productivity and fuel switching in Mozambique: Avoiding transesterification and food insecurity

This chapter explores the next steps of expanding village poultry productivity in Mozambique post control of communicable diseases by assessing co-production of edible oils and high protein poultry feeds. The production of oil was analysed from the perspective of a suitable non-fossil fuel without the need for transesterification to produce biodiesel. A range of feedstock issues were considered for co-producing vegetable oil as a fuel and high protein animal feed. Technical considerations of the direct use of straight vegetable oil (SVO) in diesel engines and oil conversion to biodiesel are discussed, and we identify more suitable options for additional mechanisation options for smallholder farmers. Potential synergies with private-public partnerships between smallholders, food production companies, and education institutions to assist introduction of new mechanisation options were investigated. The research findings indicate the lack of access to training and equipment, and also education and experience of refining bio-oil derivatives, and the parallel high demand for human and animal food/feed presented a high prospectivity of producing SVO for use in suitable engines. The chapter concludes with a strategy to maximise the potential benefits of SVO production and use within agricultural communities

Spatial Models for Field Trials

An important aim of the analysis of agricultural field trials is to obtain good predictions for genotypic performance, by correcting for spatial effects. In practice these corrections turn out to be complicated, since there can be different types of spatial effects; those due to management interventions applied to the field plots and those due to various kinds of erratic spatial trends. This paper presents models for field trials in which the random spatial component consists of tensor product Penalized splines (P-splines). A special ANOVA-type reformulation leads to five smooth additive spatial components, which form the basis of a mixed model with five unknown variance components. On top of this spatial field, effects of genotypes, blocks, replicates, and/or other sources of spatial variation are described by a mixed model in a standard way. We show the relation between several definitions of heritability and the effective dimension or the effective degrees of freedom associated to the genetic component. The approach is illustrated with large-scale field trial experiments. An R-package is provided

Development of an optimal biogas system design model for Sub-Saharan Africa with case studies from Kenya and Cameroon

The optimal biogas system design model (OBSDM) described in this paper is intended to be used as a decision-making tool to increase awareness of the potential of biogas technology for different applications in Sub-Saharan Africa (SSA). The decision-making tool identifies the most suitable biodigester design based on user defined inputs, including energy and fertiliser requirements; feedstock (type, amount, and rate of supply); water supply; land use (area, soil type, ground water level); climate (temperature and rainfall); construction materials available locally; and the priorities (based on sustainability criteria) of the intended biogas user. The output of the model provides a recommended design with estimates of the expected costs, energy and fertiliser production, and links to contact biodigester suppliers. In order to test the model, data from household surveys conducted in rural regions of Kenya and Cameroon were used as inputs to the model. An innovative fixed dome biodigester design, which uses stabilised soil blocks instead of bricks, was identified as optimal for both Kenyan and Cameroonian rural households. The expected performance of the optimal biogas system design from the model output was consistent with survey data on existing biogas systems in the region

Bodemgezondheid binnen bedrijfssystemen: BODEM

In 2006 is voor LNV het project: ‘Bodemgezondheid binnen bedrijfssystemen’ gestart. Dit project richt zich op de ontwikkeling van een pakket aan maatregelen om de bodemgezondheid te beïnvloeden

Correcting for spatial heterogeneity in plant breeding experiments with P-splines

An important aim of the analysis of agricultural field experiments is to obtain good predictions for genotypic performance, by correcting for spatial effects. In practice these corrections turn out to be complicated, since there can be different types of spatial effects; those due to management interventions applied to the field plots and those due to various kinds of erratic spatial trends. This paper explores the use of two-dimensional smooth surfaces to model random spatial variation. We propose the use of anisotropic tensor product P-splines to explicitly model large-scale (global trend) and small-scale (local trend) spatial dependence. On top of this spatial field, effects of genotypes, blocks, replicates, and/or other sources of spatial variation are described by a mixed model in a standard way. Each component in the model is shown to have an effective dimension. They are closely related to variance estimation, and helpful for characterising the importance of model components. An important result of this paper is the formal proof of the relation between several definitions of heritability and the effective dimension associated with the genetic component. The practical value of our approach is illustrated by simulations and analyses of large-scale plant breeding experiments. An \texttt{R}-package, \texttt{SpATS}, is provide