Empirical comparison of time series models and tensor product penalised splines for modelling spatial dependence in plant breeding field trials.

Plant breeding field trials are typically arranged as a row by column rectangular lattice. They have been widely analysed using linear mixed models in which low order autoregressive integrated moving average (ARIMA) time series models, and the subclass of separable lattice processes, are used to account for two-dimensional spatial dependence between the plot errors. A separable first order autoregressive model has been shown to be particularly useful in the analysis of plant breeding trials.

Meteorological and landscape influences on pollen beetle immigration into oilseed rape crops.

Heavy reliance on pesticide inputs to maintain crop yields has been an important aspect of agricultural intensification. Insecticide use has had detrimental impacts on pollinators and natural pest control agents, contributing to a decline in associated ecosystem services, and has also led to resistance development in pest populations. Throughout Europe, in oilseed rape ( L.

A hypomethylated population of Brassica rapa for forward and reverse epi-genetics.

Background: Epigenetic marks superimposed on the DNA sequence of eukaryote chromosomes provide agility and plasticity in terms of modulating gene expression, ontology, and response to the environment. Modulating the methylation status of cytosine can generate epialleles, which have been detected and characterised at specific loci in several plant systems, and have the potential to generate novel and relatively stable phenotypes. There have been no systematic attempts to explore and utilise epiallelic variation, and so extend the range of phenotypes available for selection in crop improvement.

Regulatory hotspots are associated with plant gene expression under varying soil phosphorus supply in Brassica rapa.

Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome.

To bite or not to bite! A questionnaire-based survey assessing why some people are bitten more than others by midges.

Background: The Scottish biting midge, Culicoides impunctatus, responsible for more than 90% of biting attacks on human beings in Scotland, is known to demonstrate a preference for certain human hosts over others.

Methods: In this study we used a questionnaire-based survey to assess the association between people's perception of how badly they get bitten by midges and their demographic, lifestyle and health related characteristics.

Results: Most people (85.

A novel transcriptomic approach to identify candidate genes for grain quality traits in wheat.

A novel methodology is described in which transcriptomics is combined with the measurement of bread-making quality and other agronomic traits for wheat genotypes grown in different environments (wet and cool or hot and dry conditions) to identify transcripts associated with these traits. Seven doubled haploid lines from the Spark x Rialto mapping population were selected to be matched for development and known alleles affecting quality. These were grown in polytunnels with different environments applied 14 days post-anthesis, and the whole experiment was repeated over 2 years.

Transcriptome analysis of grain development in hexaploid wheat.

Background: Hexaploid wheat is one of the most important cereal crops for human nutrition. Molecular understanding of the biology of the developing grain will assist the improvement of yield and quality traits for different environments. High quality transcriptomics is a powerful method to increase this understanding.

The analysis of longitudinal data using mixed model L-splines.

L-splines are a large family of smoothing splines defined in terms of a linear differential operator. This article develops L-splines within the context of linear mixed models and uses the resulting mixed model L-spline to analyze longitudinal data from a grassland experiment. In the spirit of time-series analysis, a periodic mixed model L-spline is developed, which partitions data into a smooth periodic component plus smooth long-term trend.