Association mapping of resistance to Puccinia hordei in Australian barley breeding germplasm

Key message “To find stable resistance using association mapping tools, QTL with major and minor effects on leaf rust reactions were identified in barley breeding lines by assessing seedlings and adult plants.” Abstract Three hundred and sixty (360) elite barley (Hordeum vulgare L.) breeding lines from the Northern Region Barley Breeding Program in Australia were genotyped with 3,244 polymorphic diversity arrays technology markers and the results used to map quantitative trait loci (QTL) conferring a reaction to leaf rust (Puccinia hordei Otth). The F3:5 (Stage 2) lines were derived or sourced from different geographic origins or hubs of international barley breeding ventures representing two breeding cycles (2009 and 2011 trials) and were evaluated across eight environments for infection type at both seedling and adult plant stages. Association mapping was performed using mean scores for disease reaction, accounting for family effects using the eigenvalues from a matrix of genotype correlations. In this study, 15 QTL were detected; 5 QTL co-located with catalogued leaf rust resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. The adult plant resistance gene Rph20 was identified across the majority of environments and pathotypes. The QTL detected in this study offer opportunities for breeding for more durable resistance to leaf rust through pyramiding multiple genomic regions via marker-assisted selection.

Lake sediment research as a part of lake management - case studies and implications from southern Finland

In Finland one of the most important current issues in the environmental management is the quality of surface waters. The increasing social importance of lakes and water systems has generated wide-ranging interest in lake restoration and management, concerning especially lakes suffering from eutrophication, but also from other environmental impacts. Most of the factors deteriorating the water quality in Finnish lakes are connected to human activities. Especially since the 1940's, the intensified farming practices and conduction of sewage waters from scattered settlements, cottages and industry have affected the lakes, which simultaneously have developed in to recreational areas for a growing number of people. Therefore, this study was focused on small lakes, which are human impacted, located close to settlement areas and have a significant value for local population. The aim of this thesis was to obtain information from lake sediment records for on-going lake restoration activities and to prove that a well planned, properly focused lake sediment study is an essential part of the work related to evaluation, target consideration and restoration of Finnish lakes. Altogether 11 lakes were studied. The study of Lake Kaljasjärvi was related to the gradual eutrophication of the lake. In lakes Ormajärvi, Suolijärvi, Lehee, Pyhäjärvi and Iso-Roine the main focus was on sediment mapping, as well as on the long term changes of the sedimentation, which were compared to Lake Pääjärvi. In Lake Hormajärvi the role of different kind of sedimentation environments in the eutrophication development of the lake's two basins were compared. Lake Orijärvi has not been eutrophied, but the ore exploitation and related acid main drainage from the catchment area have influenced the lake drastically and the changes caused by metal load were investigated. The twin lakes Etujärvi and Takajärvi are slightly eutrophied, but also suffer problems associated with the erosion of the substantial peat accumulations covering the fringe areas of the lakes. These peat accumulations are related to Holocene water level changes, which were investigated. The methods used were chosen case-specifically for each lake. In general, acoustic soundings of the lakes, detailed description of the nature of the sediment and determinations of the physical properties of the sediment, such as water content, loss on ignition and magnetic susceptibility were used, as was grain size analysis. A wide set of chemical analyses was also used. Diatom and chrysophycean cyst analyses were applied, and the diatom inferred total phosphorus content was reconstructed. The results of these studies prove, that the ideal lake sediment study, as a part of a lake management project, should be two-phased. In the first phase, thoroughgoing mapping of sedimentation patterns should be carried out by soundings and adequate corings. The actual sampling, based on the preliminary results, must include at least one long core from the main sedimentation basin for the determining the natural background state of the lake. The recent, artificially impacted development of the lake can then be determined by short-core and surface sediment studies. The sampling must be focused on the basis of the sediment mapping again, and it should represent all different sedimentation environments and bottom dynamic zones, considering the inlets and outlets, as well as the effects of possible point loaders of the lake. In practice, the budget of the lake management projects of is usually limited and only the most essential work and analyses can be carried out. The set of chemical and biological analyses and dating methods must therefore been thoroughly considered and adapted to the specific management problem. The results show also, that information obtained from a properly performed sediment study enhances the planning of the restoration, makes possible to define the target of the remediation activities and improves the cost-efficiency of the project.

Fine mapping of qGW1, a major QTL for grain weight in sorghum

Key message We detected seven QTLs for 100-grain weight in sorghum using an F 2 population, and delimited qGW1 to a 101-kb region on the short arm of chromosome 1, which contained 13 putative genes. Abstract Sorghum is one of the most important cereal crops. Breeding high-yielding sorghum varieties will have a profound impact on global food security. Grain weight is an important component of grain yield. It is a quantitative trait controlled by multiple quantitative trait loci (QTLs); however, the genetic basis of grain weight in sorghum is not well understood. In the present study, using an F2 population derived from a cross between the grain sorghum variety SA2313 (Sorghum bicolor) and the Sudan-grass variety Hiro-1 (S. bicolor), we detected seven QTLs for 100-grain weight. One of them, qGW1, was detected consistently over 2 years and contributed between 20 and 40 % of the phenotypic variation across multiple genetic backgrounds. Using extreme recombinants from a fine-mapping F3 population, we delimited qGW1 to a 101-kb region on the short arm of chromosome 1, containing 13 predicted gene models, one of which was found to be under purifying selection during domestication. However, none of the grain size candidate genes shared sequence similarity with previously cloned grain weight-related genes from rice. This study will facilitate isolation of the gene underlying qGW1 and advance our understanding of the regulatory mechanisms of grain weight. SSR markers linked to the qGW1 locus can be used for improving sorghum grain yield through marker-assisted selection.

Mapping the carriage of flaA-restriction fragment length polymorphism Campylobacter genotypes on poultry carcasses through the processing chain and comparison to clinical isolates

Poultry are considered a major source for campylobacteriosis in humans. A total of 1866 Campylobacter spp. isolates collected through the poultry processing chain were typed using flaA-restriction fragment length polymorphism to measure the impact of processing on the genotypes present. Temporally related human clinical isolates (n = 497) were also typed. Isolates were obtained from whole chicken carcass rinses of chickens collected before scalding, after scalding, before immersion chilling, after immersion chilling and after packaging as well as from individual caecal samples. A total of 32 genotypes comprising at least four isolates each were recognised. Simpson's Index of Diversity (D) was calculated for each sampling site within each flock, for each flock as a whole and for the clinical isolates. From caecal collection to after packaging samples the D value did not change in two flocks, decreased in one flock and increased in the fourth flock. Dominant genotypes occurred in each flock but their constitutive percentages changed through processing. There were 23 overlapping genotypes between clinical and chicken isolates. The diversity of Campylobacter is flock dependant and may alter through processing. This study confirms that poultry are a source of campylobacteriosis in the Australian population although other sources may contribute.

Making the most of spatial information in health: A tutorial in Bayesian disease mapping for areal data

Disease maps are effective tools for explaining and predicting patterns of disease outcomes across geographical space, identifying areas of potentially elevated risk, and formulating and validating aetiological hypotheses for a disease. Bayesian models have become a standard approach to disease mapping in recent decades. This article aims to provide a basic understanding of the key concepts involved in Bayesian disease mapping methods for areal data. It is anticipated that this will help in interpretation of published maps, and provide a useful starting point for anyone interested in running disease mapping methods for areal data. The article provides detailed motivation and descriptions on disease mapping methods by explaining the concepts, defining the technical terms, and illustrating the utility of disease mapping for epidemiological research by demonstrating various ways of visualising model outputs using a case study. The target audience includes spatial scientists in health and other fields, policy or decision makers, health geographers, spatial analysts, public health professionals, and epidemiologists.

Using relationship mapping to understand sustainable housing stakeholders’ actions

The production of sustainable housing requires the cooperation of a variety of participants with different goals, needs, levels of commitment and cultures. To achieve mainstream net zero energy housing objectives, there is arguably a need for a non-linear network of collaboration between all the stakeholders. In order to create and improve such collaborative networks between stakeholders, we first need to map stakeholders’ relationships, processes, and practices. This paper discusses compares and contrasts maps of the sustainable housing production life-cycle in Australia, developed from different perspectives. The paper highlights the strengths and weaknesses of each visualization, clarifying where gaps in connectivity exist within existing industry networks. Understanding these gaps will help researchers and practitioners identify how to improve the collaboration between participants in the housing industry. This in turn may improve decision making across all stakeholder groups, leading to mainstream implementation of sustainability into the housing industry.

Fine Mapping of qDor7, a Major QTL Affecting Seed Dormancy in Sorghum (Sorghum bicolor (L.) Moench)

Seed dormancy is a key domestication trait for major crops, which is acquired in long-term systems development processes and enables the survival of plants in adverse natural conditions. It is a complex trait under polygenic control and is affected by endogenous and environmental factors. In the present study, a major seed dormancy QTL in sorghum (Sorghum bicolor (L.) Moench), qDor7, detected previously, was fine mapped using a large, multi-generational population. The qDor7 locus was delimited to a 96-kb region which contains 16 predicted gene models. These results lay a solid foundation for cloning qDor7. In addition, the functional markers tightly linked to the seed dormancy QTL may be used in marker-assisted selection for seed dormancy in sorghum.

Mapping of assembled epitopic regions of human chorionic gonadotropin reveals proximity of CTP alpha to the determinant loop beta 93-100

Three overlapping assembled epitopes of beta hCG have been mapped using MAb probes and a single step solid phase radioimmunoassay. These epitopes have been shown to be at receptor binding region comprising of the loop region beta Cys93-Cys100. Importance of disulphide bonds in maintaining integrity of these epitopes is assessed. Two MAbs (INN 58 and INN 22) interact with the beta region as well as the alpha C-terminal peptide, while the other MAb INN 24 interacts with only the beta region. Cross-reactivity pattern with beta hCG and hLH as web as the reported crystal structure of hCG substantiates the epitope identification. The results demonstrate utility of MAbs as probes in investigations on three-dimensional structure of gonadatropins.

Coastal environmental gradients – Key to reproduction habitat mapping of freshwater fish in the Baltic Sea

Habitat requirements of fish are most strict during the early life stages, and the quality and quantity of reproduction habitats lays the basis for fish production. A considerable number of fish species in the northern Baltic Sea reproduce in the shallow coastal areas, which are also the most heavily exploited parts of the brackish marine area. However, the coastal fish reproduction habitats in the northern Baltic Sea are poorly known. The studies presented in this thesis focused on the influence of environmental conditions on the distribution of coastal reproduction habitats of freshwater fish. They were conducted in vegetated littoral zone along an exposure and salinity gradient extending from the innermost bays to the outer archipelago on the south-western and southern coasts of Finland, in the northern Baltic Sea. Special emphasis was placed on reed-covered Phragmites australis shores, which form a dominant vegetation type in several coastal archipelago areas. The main aims of this research were to (1) develop and test new survey and mapping methods, (2) investigate the environmental requirements that govern the reproduction of freshwater fish in the coastal area and (3) survey, map and model the distribution of the reproduction habitats of pike (Esox lucius) and roach (Rutilus rutilus). The white plate and scoop method with a standardized sampling time and effort was demonstrated to be a functional method for sampling the early life stages of fish in dense vegetation and shallow water. Reed-covered shores were shown to form especially important reproduction habitats for several freshwater fish species, such as pike, roach, other cyprinids and burbot, in the northern Baltic Sea. The reproduction habitats of pike were limited to sheltered reed- and moss-covered shores of the inner and middle archipelago, where suitable zooplankton prey were available and the influence of the open sea was low. The reproduction habitats of roach were even more limited and roach reproduction was successful only in the very sheltered reed-covered shores of the innermost bay areas, where salinity remained low (< 4‰) during the spawning season due to freshwater inflow. After identifying the critical factors restricting the reproduction of pike and roach, the spatial distribution of their reproduction habitats was successfully mapped and modelled along the environmental gradients using only a few environmental predictor variables. Reproduction habitat maps are a valuable tool promoting the sustainable use and management of exploited coastal areas and helping to maintain the sustainability of fish populations. However, the large environmental gradients and the extensiveness of the archipelago zone in the northern Baltic Sea demand an especially high spatial resolution of the coastal predictor variables. Therefore, the current lack of accurate large-scale, high-resolution spatial data gathered at exactly the right time is a considerable limitation for predictive modelling of shallow coastal waters.

Mapping of assembled epitopes with microgram quantities of antigen: Identification of an epitope at the receptor binding region of human follicle stimulating hormone

Identification of epitopes by modification studies has been reported by us recently. The method requires milligram quantities of antigen and since several proteins are not available in large quantities they are not amenable for such an investigation. One such protein is human follicle stimulating hormone (hFSH) whose mapping of epitopes is of importance in reproductive biology. Here we report a method that uses microgram quantities of hFSH to map a beta-specific epitope located at the receptor binding region. This identification has also been validated by the chemical modification method using heterologous antigen ovine follicle stimulating hormone (oFSH).