Non-iterative variance component estimation in QTL analysis

In variance component quantitative trait loci (QTL) analysis, a mixed model is used to detect the most likely chromosome position of a QTL. The putative QTL is included as a random effect and a method is needed to estimate the QTL variance. The standard estimation method used is an iterative method based on the restricted maximum likelihood (REML). In this paper, we present a novel non-iterative variance component estimation method. This method is based on Henderson's method 3, but relaxes the condition of unbiasedness. Two similar estimators were compared, which were developed from two different partitions of the sum of squares in Henderson's method 3. The approach was compared with REML on data from a European wild boar × domestic pig intercross. A meat quality trait was studied on chromosome 6 where a functional gene was known to be located. Both partitions resulted in estimated QTL variances close to the REML estimates. From the non-iterative estimates, we could also compute good approximations of the likelihood ratio curve on the studied chromosome.     

Effects of inter-varietal diversity,biotic stresses and environmental productivity on grain yield of spring barley variety mixtures

Varietal seed mixtures tend to increase and stabilize crop yields, yet their application is sparse. Large-scale cultivation of variety mixtures may require a better understanding of how inter-varietal interactions and their interaction with the environment may influence the grain yield of variety mixtures relative to their component varieties. For this purpose, six variety mixtures of spring barley and 14 component varieties were grown in each of 17 trial environments. A total of 28 observed and a priori plant characteristics, including grain yield, disease severity and weed competitiveness, were derived for each component variety in each trial. The relationship between inter-varietal diversity of each characteristic and the mixing effect on grain yield was analysed. Additionally, various types of yield stability were estimated and compared among mixtures and component varieties. One mixture out-yielded all of its component varieties in almost half of the trial environments. Inter-varietal diversity in grain yield potential correlated significantly with mixing effect, as did straw length diversity when weighted with weed pressure. The grain yields of most mixtures were more stable across environments than their component varieties when accounting also for the general response to environmental productivity. Hence, most mixtures adapted slightly better to environmental productivity and were less sensitive to environmental stress than their component varieties. We conclude that the efficacy of variety mixtures may be enhanced by mixing relatively high-yielding varieties differing in responsiveness to environmental productivity.     

Valuation of salmon farming companies

Financial statement information is important for evaluating a firm’s performance, and for forecasting its future cash flows. This paper studies the relationship between financial accounting information and market valuation for publicly listed salmon farming companies. Of special interest is the impact on market valuation, of a requirement for salmon farmers to disclose the effect on their financial numbers of the fair-value adjustment of biomass. The results suggest that the fair-value adjustment results in higher volatility of profits, and lower value relevance for investors.     

Demand feeding and welfare in farmed fish

Following the development of demand-feeding systems, many experiments have been conducted to explore feeding motivation and feed intake in farmed fish. This work aims to review a selection of studies in the field, focusing on three key factors, related to demand feeding and fish welfare. Firstly, we outline how demand feeders should be considered when developing feed management strategies for improving welfare in production conditions. Secondly, via laboratory demand-feeding experiments, we show self-feeding activities depend not only on feeding motivation and social organisation, but also on individual learning capacity and risk-taking behaviour. Thirdly, we report encouraging results demonstrating that when presented with two or more self-feeders containing complementary foods, fish select a diet according to their specific nutritional requirements, suggesting that demand feeders could be used to improve welfare by allowing fish to meet their nutritional needs.     

Starved bacteria retain their size but lose culturability - Lessons from a 5000 years old undisturbed A-horizon

The vast majority of soil bacteria are unable to form visible colonies on agar media. One hypothesis is that unculturable soil bacteria are dwarf cells that may either be small starved forms derived from larger species or represent inherently small species. We test the hypotheses that cells of extremely starved soil bacterial communities are smaller and less culturable than cells of bacterial communities from a richer soil, and that culturability is related to cell size by comparing an extremely starved community from a 5200-year-old A-horizon buried under a burial mound with a community from a modern agricultural A-horizon.We serially filtered cell suspensions through filters with successively smaller pore sizes (0.8 μm, 0.6 μm and 0.4 μm) and assessed total cell number and culturability, i.e. the ability to form colonies on two types of agar media, in each size fraction. Cell size distributions were assessed in unfiltered suspensions. Average cell size was only moderately reduced in the starved community, where culturability was low for all size classes. In contrast, culturability was much higher in the modern community, where culturability decreased dramatically with decreasing cell sizes.     

Predicting spring barley yield from variety-specific yield potential, disease resistance and straw length, and from environment-specific disease loads and weed pressure

For low-input crop production, well-characterised varieties increase the possibilities of managing diseases and weeds. This analysis aims at developing a framework for analyzing grain yield using external varietal information about disease resistance, weed competitiveness and yield potential and quantifying the impact of susceptibility grouping and straw length scores (as a measure for weed competitiveness) for predicting spring barley grain yield under variable biotic stress levels. The study comprised 52 spring barley varieties and 17 environments, i.e., combinations of location, growing system and year. Individual varieties and their interactions with environments were analysed by factorial regression of grain yield on external variety information combined with observed environmental disease loads and weed pressure. The external information was based on the official Danish VCU testing. The most parsimonious models explained about 50% of the yield variation among varieties including genotype-environment interactions. Disease resistance characteristics of varieties, weighted with disease loads of powdery mildew, leaf rust and net blotch, respectively, had a highly significant influence on grain yield. The extend to which increased susceptibility resulted in increased yield losses in environments with high disease loads of the respective diseases was predicted. The effect of externally determined straw length scores, weighted with weed pressure, was weaker although significant for weeds with creeping growth habit. Higher grain yield was thus predicted for taller plants under weed pressure. The results are discussed in relation to the model framework, impact of the considered traits and use of information from conventional variety testing in organic cropping systems.