Trade-offs in the genetic control of functional and nutritional quality traits in UK winter wheat

A complex network of trade-offs exists between wheat quality and nutritional traits. We investigated the correlated relationships among several milling and baking traits as well as mineral density in refined white and whole grain flour. Our aim was to determine their pleiotropic genetic control in a multi-parent population over two trial years with direct application to practical breeding. Co-location of major quantitative trait loci (QTL) and principal component based multi-trait QTL mapping increased the power to detect QTL and revealed pleiotropic effects explaining many complementary and antagonistic trait relationships. High molecular weight glutenin subunit genes explained much of the heritable variation in important dough rheology traits, although additional QTL were detected. Several QTL, including one linked to the TaGW2 gene, controlled grain size and increased flour extraction rate. The semi-dwarf Rht-D1b allele had a positive effect on Hagberg falling number, but reduced grain size, specific weight, grain protein content and flour water absorption. Mineral nutrient concentrations were lower in Rht-D1b lines for many elements, in wholemeal and white flour, but potassium concentration was higher in Rht-D1b lines. The presence of awns increased calcium content without decreasing extraction rate, despite the negative correlation between these traits. QTL were also found that affect the relative concentrations of key mineral nutrients compared to phosphorus which may help increase bioavailability without associated anti-nutritional effects of phytic acid. Taken together these results demonstrate the potential for marker-based selection to optimise trait trade-offs and enhance wheat nutritional value by considering pleiotropic genetic effects across multiple traits.Subject terms: Plant breeding, Quantitative trait, Genetic variation     

Maternal transfer of strain-specific immunity in an invertebrate

The most celebrated component of the vertebrate immune system is the acquired response in which memory cells established during primary infection enhance the proliferation of antibodies during secondary infection. Additionally, the strength of vertebrate acquired immune responses varies dramatically depending on the infecting pathogen species or on the pathogen genotype within species. Because invertebrates lack the T-cell receptors and Major Histocompatibility Complex (MHC) molecules that mediate vertebrate adaptive immune responses, they are thought to lack adaptive immunity and be relatively unspecific in their interactions with pathogens. With only innate immunity, invertebrate hosts are believed to be nai;ve at each new encounter with pathogens. Nevertheless, some forms of facultative immunity appear to be important in insects; some individuals have enhanced immunity due to population density, and some social insects benefit when their nest-mates have been exposed to a pathogen or pathogen mimic (; see for a predation example.) Here we provide evidence for acquired strain-specific immunity in the crustacean Daphnia magna infected with the pathogenic bacteria Pasteuria ramosa. Specifically, the fitness of hosts was enhanced when challenged with a bacterial strain their mother had experienced relative to cases when mother and offspring were challenged with different strains.     

Xylem cavitation vulnerability influences tree species’ habitat preferences in miombo woodlands

Although precipitation plays a central role in structuring Africa’s miombo woodlands, remarkably little is known about plant-water relations in this seasonally dry tropical forest. Therefore, in this study, we investigated xylem vulnerability to cavitation for nine principal tree species of miombo woodlands, which differ in habitat preference and leaf phenology. We measured cavitation vulnerability (Ψ₅₀), stem-area specific hydraulic conductivity (K _S), leaf specific conductivity (K _L), seasonal variation in predawn water potential (Ψ_PD) and xylem anatomical properties [mean vessel diameter, mean hydraulic diameter, mean hydraulic diameter accounting for 95 % flow, and maximum vessel length (V _L)]. Results show that tree species with a narrow habitat range (mesic specialists) were more vulnerable to cavitation than species with a wide habitat range (generalists). Ψ₅₀ for mesic specialists ranged between ?1.5 and ?2.2 MPa and that for generalists between ?2.5 and ?3.6 MPa. While mesic specialists exhibited the lowest seasonal variation in Ψ_PD, generalists displayed significant seasonal variations in Ψ_PD suggesting that the two miombo habitat groups differ in their rooting depth. We observed a strong trade-off between K _S and Ψ₅₀ suggesting that tree hydraulic architecture is one of the decisive factors setting ecological boundaries for principal miombo species. While vessel diameters correlated weakly (P > 0.05) with Ψ₅₀, V _L was positively and significantly correlated with Ψ₅₀. Ψ_PD was significantly correlated with Ψ₅₀ further reinforcing the conclusion that tree hydraulic architecture plays a significant role in species’ habitat preference in miombo woodlands.     

Annexin-mediated secretory vesicle aggregation in plants

The mechanism by which membranes fuse during vesicle-mediated secretion is of considerable importance for plant cell growth, but remains unknown. We have identified Ca²⁺-dependent phospholipid-binding proteins (annexins) from maize ( Zea mays ), that may play a part in this process. An assay for Ca²⁺-dependent binding of annexins to liposomes, revealed that the maize proteins (p23, p33 and p35) and annexins from bovine lung, bind over a similar range of Ca²⁺ concentrations. Turbidity assays further revealed that both maize and bovine annexins induced liposome aggregation and that the plant annexins were also effective at aggregating plant secretory vesicles. This aggregation occurred at levels of free Ca²⁺ similar to that required for the binding of annexins p33 and p35. We discuss the significance of these results for the plant secretory apparatus.     

Mapping ephemeral wetlands: manual digitisation and logistic regression modelling in Nelson Mandela Bay Municipality,South Africa

Until recently, little research has been conducted on the distribution and structure of ephemeral systems in semi-arid areas. This information is critical for appropriate wetland management and conservation. The Nelson Mandela Bay Municipality is a semi-arid area along the south-eastern coastline of the Eastern Cape Province of South Africa. The Municipality encapsulates a wide range of geological and geomorphological features as well as vegetation types within an area of some 1950 km², providing an ideal area for such research. The distribution and abundance of wetlands were defined, and a logistic regression (LR) model was used to establish whether this modelling technique is viable in semi-arid areas with highly variable rainfall patterns. Wetlands were delineated manually using geographical information systems, high-resolution aerial photographs and environmental data. More than 1700 wetland polygons were identified, with 80% of the systems being categorised as depressions, seeps and wetland flats. Unchannelled (8%) and channelled (7%) valley bottom wetlands and floodplain wetlands (5%) were also identified. The wetland database was then used to create a wetland occurrence probability model. There were 19 environmental variables used to develop the LR model, with eight variables used in the final model output. The predictive capacity of the model was good, with an area under curve value of 0.68 and an overall accuracy of 66%. This indicates that probabilistic wetland models are useful in highly variable environments with high numbers of small (<1 ha) wetlands. Such predictive models provide a tool to assist in improving the accuracy of land cover datasets in semi-arid areas, and can be used to inform management decisions on flood risk areas and key conservation zones. In addition, abiotic variables that are significant in the model output provide an indication of the factors influencing wetland functioning in the region.     

Rapid mapping and identification of mutations in Caenorhabditis elegans by restriction site-associated DNA mapping and genomic interval pull-down sequencing

Forward genetic screens provide a powerful approach for inferring gene function on the basis of the phenotypes associated with mutated genes. However, determining the causal mutation by traditional mapping and candidate gene sequencing is often the rate-limiting step, especially when analyzing many mutants. We report two genomic approaches for more rapidly determining the identity of the affected genes in Caenorhabditis elegans mutants. First, we report our use of restriction site-associated DNA (RAD) polymorphism markers for rapidly mapping mutations after chemical mutagenesis and mutant isolation. Second, we describe our use of genomic interval pull-down sequencing (GIPS) to selectively capture and sequence megabase-sized portions of a mutant genome. Together, these two methods provide a rapid and cost-effective approach for positional cloning of C. elegans mutant loci, and are also applicable to other genetic model systems.     

Flow cytometry and FACS applied to filamentous fungi

Flow cytometry is an automated, laser- or impedance-based, high throughput method that allows very rapid analysis of multiple chemical and physical characteristics of single cells within a cell population. It is an extremely powerful technology that has been used for over four decades with filamentous fungi. Although single cells within a cell population are normally analysed rapidly on a cell-by-cell basis using the technique, flow cytometry can also be used to analyse cell (e.g. spore) aggregates or entire microcolonies. Living or fixed cells can be stained with a wide range of fluorescent reporters to label different cell components or measure different physiological processes. Flow cytometry is also suited for measurements of cell size, interaction, aggregation or shape using non-labelled cells by means of analysing their light scattering characteristics. Fluorescence-activated cell sorting (FACS) is a specialized form of flow cytometry that provides a method for sorting a heterogeneous mixture of cells into two or more containers based upon the fluorescence and/or light scattering properties of each cell. The major advantage of analysing cells by flow cytometry over microscopy is the speed of analysis: thousands of cells can be analysed per second or sorted in minutes. Drawbacks of flow cytometry are that specific cells cannot be followed in time and normally spatial information relating to individual cells is lacking. A big advantage over microscopy is when using FACS, cells with desired characteristics can be sorted for downstream experimentation (e.g. for growth, infection, enzyme production, gene expression assays or ‘omics’ approaches). In this review, we explain the basic concepts of flow cytometry and FACS, define its advantages and disadvantages in comparison with microscopy, and describe the wide range of applications in which these powerful technologies have been used with filamentous fungi.     

Physiological and molecular diversity of feather moss associative N2-fixing cyanobacteria

Cyanobacteria colonizing the feather moss Pleurozium schreberi were isolated from moss samples collected in northern Sweden and subjected to physiological and molecular characterization. Morphological studies of isolated and moss-associated cyanobacteria were carried out by light microscopy. Molecular tools were used for cyanobacteria identification, and a reconstitution experiment of the association between non-associative mosses and cyanobacteria was conducted. The influence of temperature on N2 fixation in the different cyanobacterial isolates and the influence of light and temperature on N2-fixation rates in the moss were studied using the acetylene reduction assay. Two different cyanobacteria were effectively isolated from P. schreberi: Nostoc sp. and Calothrix sp. A third genus, Stigonema sp. was identified by microscopy, but could not be isolated. The Nostoc sp. was found to fix N2 at lower temperatures than Calothrix sp. Nostoc sp. and Stigonema sp. were the predominant cyanobacteria colonizing the moss. The attempt to reconstitute the association between the moss and cyanobacteria was successful. The two isolated genera of cyanobacteria in feather moss samples collected in northern Sweden differ in their temperature optima, which may have important ecological implications.     

Persistence and Expression of the Herpes Simplex Virus Genome in the Absence of Immediate-Early Proteins

The immediate-early (IE) proteins of herpes simplex virus (HSV) function on input genomes and affect many aspects of host cell metabolism to ensure the efficient expression and regulation of the remainder of the genome and, subsequently, the production of progeny virions. Due to the many and varied effects of IE proteins on host cell metabolism, their expression is not conducive to normal cell function and viability. This presents a major impediment to the use of HSV as a vector system. In this study, we describe a series of ICP4 mutants that are defective in different subsets of the remaining IE genes. One mutant, d109, does not express any of the IE proteins and carries a green fluorescent protein (GFP) transgene under the control of the human cytomegalovirus IE promoter (HCMVIEp). d109 was nontoxic to Vero and human embryonic lung (HEL) cells at all multiplicities of infection tested and was capable of establishing persistent infections in both of these cell types. Paradoxically, the genetic manipulations that were required to eliminate toxicity and allow the genome to persist in cells for long periods of time also dramatically lowered the level of transgene expression. Efficient expression of the HCMVIEp-GFP transgene in the absence of ICP4 was dependent on the ICP0 protein. In d109-infected cells, the level of transgene expression was very low in most cells but abundant in a small subpopulation of cells. However, expression of the transgene could be induced in cells containing quiescent d109 genomes weeks after the initial infection, demonstrating the functionality of the persisting genomes.