HUN-REN Centre for Agricultural Research

An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.

The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV.

Abstract Grassland diversity can support sustainable intensification of grassland production through increased yields, reduced inputs and limited weed invasion. We report the effects of diversity on weed suppression from 3 years of a 31‐site continental‐scale field experiment. At each site, 15 grassland communities comprising four monocultures and 11 four‐species mixtures based on a wide range of species' proportions were sown at two densities and managed by cutting. Forage species were selected according to two crossed functional traits, “method of nitrogen acquisition” and “pattern of temporal development”. Across sites, years and sown densities, annual weed biomass in mixtures and monocultures was 0.5 and 2.0 t DM ha −1 (7% and 33% of total biomass respectively). Over 95% of mixtures had weed biomass lower than the average of monocultures, and in two‐thirds of cases, lower than in the most suppressive monoculture (transgressive suppression). Suppression was significantly transgressive for 58% of site‐years. Transgressive suppression by mixtures was maintained across years, independent of site productivity. Based on models, average weed biomass in mixture over the whole experiment was 52% less (95% confidence interval: 30%–75%) than in the most suppressive monoculture. Transgressive suppression of weed biomass was significant at each year across all mixtures and for each mixture. Weed biomass was consistently low across all mixtures and years and was in some cases significantly but not largely different from that in the equiproportional mixture. The average variability (standard deviation) of annual weed biomass within a site was much lower for mixtures (0.42) than for monocultures (1.77). Synthesis and applications . Weed invasion can be diminished through a combination of forage species selected for complementarity and persistence traits in systems designed to reduce reliance on fertiliser nitrogen. In this study, effects of diversity on weed suppression were consistently strong across mixtures varying widely in species' proportions and over time. The level of weed biomass did not vary greatly across mixtures varying widely in proportions of sown species. These diversity benefits in intensively managed grasslands are relevant for the sustainable intensification of agriculture and, importantly, are achievable through practical farm‐scale actions.

Environmental monitoring plays a central role in diagnosing climate and management impacts on natural and agricultural systems; enhancing the understanding of hydrological processes; optimizing the allocation and distribution of water resources; and assessing, forecasting, and even preventing natural disasters. Nowadays, most monitoring and data collection systems are based upon a combination of ground-based measurements, manned airborne sensors, and satellite observations. These data are utilized in describing both small- and large-scale processes, but have spatiotemporal constraints inherent to each respective collection system. Bridging the unique spatial and temporal divides that limit current monitoring platforms is key to improving our understanding of environmental systems. In this context, Unmanned Aerial Systems (UAS) have considerable potential to radically improve environmental monitoring. UAS-mounted sensors offer an extraordinary opportunity to bridge the existing gap between field observations and traditional air- and space-borne remote sensing, by providing high spatial detail over relatively large areas in a cost-effective way and an entirely new capacity for enhanced temporal retrieval. As well as showcasing recent advances in the field, there is also a need to identify and understand the potential limitations of UAS technology. For these platforms to reach their monitoring potential, a wide spectrum of unresolved issues and application-specific challenges require focused community attention. Indeed, to leverage the full potential of UAS-based approaches, sensing technologies, measurement protocols, postprocessing techniques, retrieval algorithms, and evaluation techniques need to be harmonized. The aim of this paper is to provide an overview of the existing research and applications of UAS in natural and agricultural ecosystem monitoring in order to identify future directions, applications, developments, and challenges.

Fungi and plants are rich sources of thousands of secondary metabolites. The genetically coded possibilities for secondary metabolite production, the stimuli of the production, and the special phytotoxins basically determine the microscopic fungi-host plant interactions and the pathogenic lifestyle of fungi. The review introduces plant secondary metabolites usually with antifungal effect as well as the importance of signaling molecules in induced systemic resistance and systemic acquired resistance processes. The review also concerns the mimicking of plant effector molecules like auxins, gibberellins and abscisic acid by fungal secondary metabolites that modulate plant growth or even can subvert the plant defense responses such as programmed cell death to gain nutrients for fungal growth and colonization. It also looks through the special secondary metabolite production and host selective toxins of some significant fungal pathogens and the plant response in form of phytoalexin production. New results coming from genome and transcriptional analyses in context of selected fungal pathogens and their hosts are also discussed.

Abstract Soil, through its various functions, plays a vital role in the Earth's ecosystems and provides multiple ecosystem services to humanity. Pedotransfer functions (PTFs) are simple to complex knowledge rules that relate available soil information to soil properties and variables that are needed to parameterize soil processes. In this paper, we review the existing PTFs and document the new generation of PTFs developed in the different disciplines of Earth system science. To meet the methodological challenges for a successful application in Earth system modeling, we emphasize that PTF development has to go hand in hand with suitable extrapolation and upscaling techniques such that the PTFs correctly represent the spatial heterogeneity of soils. PTFs should encompass the variability of the estimated soil property or process, in such a way that the estimation of parameters allows for validation and can also confidently provide for extrapolation and upscaling purposes capturing the spatial variation in soils. Most actively pursued recent developments are related to parameterizations of solute transport, heat exchange, soil respiration, and organic carbon content, root density, and vegetation water uptake. Further challenges are to be addressed in parameterization of soil erosivity and land use change impacts at multiple scales. We argue that a comprehensive set of PTFs can be applied throughout a wide range of disciplines of Earth system science, with emphasis on land surface models. Novel sensing techniques provide a true breakthrough for this, yet further improvements are necessary for methods to deal with uncertainty and to validate applications at global scale.

Abstract This fascinating book describes an ongoing study of a large group of red deer (Cervus elaphus) on Rhum, an island off the west coast of Scotland.

Plant glutathione S-transferases (GSTs) are ubiquitous and multifunctional enzymes encoded by large gene families. A characteristic feature of GST genes is their high inducibility by a wide range of stress conditions including biotic stress. Early studies on the role of GSTs in plant biotic stress showed that certain GST genes are specifically up-regulated by microbial infections. Later numerous transcriptome-wide investigations proved that distinct groups of GSTs are markedly induced in the early phase of bacterial, fungal and viral infections. Proteomic investigations also confirmed the accumulation of multiple GST proteins in infected plants. Furthermore, functional studies revealed that overexpression or silencing of specific GSTs can markedly modify disease symptoms and also pathogen multiplication rates. However, very limited information is available about the exact metabolic functions of disease-induced GST isoenzymes and about their endogenous substrates. The already recognized roles of GSTs are the detoxification of toxic substances by their conjugation with glutathione, the attenuation of oxidative stress and the participation in hormone transport. Some GSTs display glutathione peroxidase activity and these GSTs can detoxify toxic lipid hydroperoxides that accumulate during infections. GSTs can also possess ligandin functions and participate in the intracellular transport of auxins. Notably, the expression of multiple GSTs is massively activated by salicylic acid and some GST enzymes were demonstrated to be receptor proteins of salicylic acid. Furthermore, induction of GST genes or elevated GST activities have often been observed in plants treated with beneficial microbes (bacteria and fungi) that induce a systemic resistance response (ISR) to subsequent pathogen infections. Further research is needed to reveal the exact metabolic functions of GST isoenzymes in infected plants and to understand their contribution to disease resistance.

Providing an adequate quantity and quality of food for the escalating human population under changing climatic conditions is currently a great challenge. In outdoor cultures, sunlight provides energy (through photosynthesis) for photosynthetic organisms. They also use light quality to sense and respond to their environment. To increase the production capacity, controlled growing systems using artificial lighting have been taken into consideration. Recent development of light-emitting diode (LED) technologies presents an enormous potential for improving plant growth and making systems more sustainable. This review uses selected examples to show how LED can mimic natural light to ensure the growth and development of photosynthetic organisms, and how changes in intensity and wavelength can manipulate the plant metabolism with the aim to produce functionalized foods.

This paper addresses the challenges of the transition from a fossil fuel-dependent to a bio-based economy and implications related to the production of food, feed, bioenergy and other bio-based materials. The objective is to provide a comprehensive review of global biomass and biomass-based energy supplies and demand, with particular attention to the EU. Furthermore, factors related to setting priorities in the use of non-food biomass are discussed, as food security will remain the top priority. Finally, the changes in the bioenergy balance indicators in the Member States of the EU and new plant breeding technologies are analyzed. Overall, this study describes the complexity of the bio-based value chains in making decisions on how best to use biomass. The article presents a comprehensive review on global biomass and biomass based energy supplies and demand, discusses the European chemical industry perspective, analyzes the changes in the biomass based energy balance indicators in the Member States of the EU, and considers the challenges of the new plant breeding technologies.

Soil contamination is one of the greatest concerns among the threats to soil resources in Europe and globally. Despite of its importance there was only very course scale (1/5000km(2)) data available on soil heavy metal concentrations prior to the LUCAS topsoil survey, which had a sampling density of 200km(2). Based on the results of the LUCAS sampling and auxiliary information detailed and up-to-date maps of heavy metals (As, Cd, Cr, Cu, Hg, Pb, Zn, Sb, Co and Ni) in the topsoil of the European Union were produced. Using the maps of heavy metal concentration in topsoil we made a spatial prediction of areas where local assessment is suggested to monitor and eventually control the potential threat from heavy metals. Most of the examined elements remain under the corresponding threshold values in the majority of the land of the EU. However, one or more of the elements exceed the applied threshold concentration on 1.2Mkm(2), which is 28.3% of the total surface area of the EU. While natural backgrounds might be the reason for high concentrations on large proportion of the affected soils, historical and recent industrial and mining areas show elevated concentrations (predominantly of As, Cd, Pb and Hg) too, indicating the magnitude of anthropogenic effect on soil quality in Europe.

Abstract Understanding the drivers of yield levels under climate change is required to support adaptation planning and respond to changing production risks. This study uses an ensemble of crop models applied on a spatial grid to quantify the contributions of various climatic drivers to past yield variability in grain maize and winter wheat of European cropping systems (1984–2009) and drivers of climate change impacts to 2050. Results reveal that for the current genotypes and mix of irrigated and rainfed production, climate change would lead to yield losses for grain maize and gains for winter wheat. Across Europe, on average heat stress does not increase for either crop in rainfed systems, while drought stress intensifies for maize only. In low-yielding years, drought stress persists as the main driver of losses for both crops, with elevated CO 2 offering no yield benefit in these years.

Abstract Antlers are complex organs which normally cast and regrow annually; they are the only regular mammalian example of organ regeneration. Richard Goss, of Brown University, Rhode Island, has had a long and absorbing interest in these ineredible tissues, and of those currently involved in antler research he is one of the most qualified to write a book. This is the fourth major work on antlers in the past 20 years, * although one (Bubenik, 1966), was not published in English. Within the last few years, there has been an upsurge of interest in antlers, and a considerable amount of new work published; Goss has performed a useful task in assembling and interpreting much of it. Having said that, I still feel that this intriguing book is really unfinished: it lacks a final chapter, which would have given the reader some challenges to consider, to reflect on and to act on. The jacket statement reads: “Students of development, evolution and behaviour will find much to appreciate in this volume, as will ecologists, wildlife biologists and zookeepers… endocrinologists, physiologists… orthopedists… pharmacologists”. While this is true, a person of Goss's capabilities could have given them a lot more. However the book is still a very good one especially for those wishing to know more about antlers, and where to find out. In New Zealand, it should also find a ready audience within the deer farming industry, since much of it could be read and understood by non‐scientific readers.

A range of continental-scale soil datasets exists in Europe with different spatial representation and based on different principles. We developed comprehensive pedotransfer functions (PTFs) for applications principally on spatial datasets with continental coverage. The PTF development included the prediction of soil water retention at various matric potentials and prediction of parameters to characterize soil moisture retention and the hydraulic conductivity curve (MRC and HCC) of European soils. We developed PTFs with a hierarchical approach, determined by the input requirements. The PTFs were derived by using three statistical methods: (i) linear regression where there were quantitative input variables, (ii) a regression tree for qualitative, quantitative and mixed types of information and (iii) mean statistics of developer-defined soil groups (class PTF) when only qualitative input parameters were available. Data of the recently established European Hydropedological Data Inventory (EU-HYDI), which holds the most comprehensive geographical and thematic coverage of hydro-pedological data in Europe, were used to train and test the PTFs. The applied modelling techniques and the EU-HYDI allowed the development of hydraulic PTFs that are more reliable and applicable for a greater variety of input parameters than those previously available for Europe. Therefore the new set of PTFs offers tailored advanced tools for a wide range of applications in the continent.

Virus taxonomy emerged as a discipline in the middle of the twentieth century. Traditionally, classification by virus taxonomists has been focussed on the grouping of relatively closely related viruses. However, during the past few years, the International Committee on Taxonomy of Viruses (ICTV) has recognized that the taxonomy it develops can be usefully extended to include the basal evolutionary relationships among distantly related viruses. Consequently, the ICTV has changed its Code to allow a 15-rank classification hierarchy that closely aligns with the Linnaean taxonomic system and may accommodate the entire spectrum of genetic divergence in the virosphere. The current taxonomies of three human pathogens, Ebola virus, severe acute respiratory syndrome coronavirus and herpes simplex virus 1 are used to illustrate the impact of the expanded rank structure. This new rank hierarchy of virus taxonomy will stimulate further research on virus origins and evolution, and vice versa, and could promote crosstalk with the taxonomies of cellular organisms.

After the era of plentiful antibiotics we are alarmed by the increasing number of antibiotic resistant strains. The genetic flexibility and adaptability of Escherichia coli to constantly changing environments allows to acquire a great number of antimicrobial resistance mechanisms. Commensal strains of E. coli as versatile residents of the lower intestine are also repeatedly challenged by antimicrobial pressures during the lifetime of their host. As a consequence, commensal strains acquire the respective resistance genes, and/or develop resistant mutants in order to survive and maintain microbial homeostasis in the lower intestinal tract. Thus, commensal E. coli strains are regarded as indicators of antimicrobial load on their hosts. This chapter provides a short historic background of the appearance and presumed origin and transfer of antimicrobial resistance genes in commensal intestinal E. coli of animals with comparative information on their pathogenic counterparts. The dynamics, development, and ways of evolution of resistance in the E. coli populations differ according to hosts, resistance mechanisms, and antimicrobial classes used. The most frequent tools of E. coli against a variety of antimicrobials are the efflux pumps and mobile resistance mechanisms carried by plasmids and/or other transferable elements. The emergence of hybrid plasmids (both resistance and virulence) among E. coli is of further concern. Co-existence and co-transfer of these "bad genes" in this huge and most versatile in vivo compartment may represent an increased public health risk in the future. Significance of multidrug resistant (MDR) commensal E. coli seem to be highest in the food animal industry, acting as reservoir for intra- and interspecific exchange and a source for spread of MDR determinants through contaminated food to humans. Thus, public health potential of MDR commensal E. coli of food animals can be a concern and needs monitoring and more molecular analysis in the future.

1. Vegetative secondary growth Lotus pedunculatus was cut daily, and fed fresh at hourly intervals (600 g dry matter (DM)/d) to three groups each of three sheep fitted with permanent cannulas into the rumen and duodenum. Lotus fed to two of the groups was sprayed with low and high rates of polyethylene glycol (PEG; molecular weight 3350), which specifically binds the condensed tannins (CT). Nutrient intake and faecal excretion were measured directly, duodenal flows estimated from continuous intraruminal infusion of inert ruthenium phenanthroline (Ru-P) and CrEDTA markers, and rumen pool sizes measured at slaughter. 2. Dietary concentrations of total reactive CT (i.e. that not bound to PEG) were 95, 45 and 14 g/kg DM, whilst the corresponding values for free CT were 15, 5 and 2 g/kg DM. 3. Increasing dietary reactive CT concentration linearly increased duodenal flows of non-ammonia nitrogen, but linearly decreased the apparent digestibility of energy and organic matter, and rumen digestion of hemicellulose but not of cellulose. Rumen digestion as a proportion of total digestion was increased by the higher PEG rate for organic matter, energy, pectin and lignin. 4. High dietary CT concentration was associated with increased N retention. Rumen ammonia concentration and pool size showed only a slight decline on this diet, indicating that there must have been increased recycling of N into the rumen. 5. Increasing dietary reactive CT concentration had no effect on the rate at which carbohydrate constituents were degraded in the rumen per unit time (FDR), but increased the rate at which their undegraded residues (FOR) left the rumen per unit time. The latter appeared to be the principal mechanism by which rumen digestion as a proportion of total digestion was reduced at high dietary CT concentrations. From a comparison of FDR and FOR of carbohydrate components in lotus and Brassica oleracea diets, it was concluded that hemicellulose digestion was rate-limiting for rumen cell-wall digestion, probably due to bonding with lignin. However, the considerable post-rumen digestion of hemicellulose was not associated with post-rumen lignin digestion. 6. It was concluded that a desired concentration of CT in Lotus sp. should represent a balance between the positive effect of CT in improving the efficiency of N digestion and their negative effect in depressing rumen carbohydrate digestion. A recommended concentration is 30-40 g/kg DM.

Plant growth-promoting bacteria play an essential role in enhancing the physical, chemical and biological characters of soils by facilitating nutrient uptake and water flow, especially under abiotic stress conditions, which are major constrains to agricultural development and production. Drought is one of the most harmful abiotic stress and perhaps the most severe problem facing agricultural sustainability, leading to a severe shortage in crop productivity. Drought affects plant growth by causing hormonal and membrane stability perturbations, nutrient imbalance and physiological disorders. Furthermore, drought causes a remarkable decrease in leaf numbers, relative water content, sugar yield, root yield, chlorophyll a and b and ascorbic acid concentrations. However, the concentrations of total phenolic compounds, electrolyte leakage, lipid peroxidation, amounts of proline, and reactive oxygen species are considerably increased because of drought stress. This negative impact of drought can be eliminated by using plant growth-promoting bacteria (PGPB). Under drought conditions, application of PGPB can improve plant growth by adjusting hormonal balance, maintaining nutrient status and producing plant growth regulators. This role of PGPB positively affects physiological and biochemical characteristics, resulting in increased leaf numbers, sugar yield, relative water content, amounts of photosynthetic pigments and ascorbic acid. Conversely, lipid peroxidation, electrolyte leakage and amounts of proline, total phenolic compounds and reactive oxygen species are decreased under drought in the presence of PGPB. The current review gives an overview on the impact of drought on plants and the pivotal role of PGPB in mitigating the negative effects of drought by enhancing antioxidant defense systems and increasing plant growth and yield to improve sustainable agriculture.

Environmental monitoring plays a central role in diagnosing climate and management impacts on natural and agricultural systems, enhancing the understanding hydrological processes, optimizing the allocation and distribution of water resources, and assessing, forecasting and even preventing natural disasters. Nowadays, most monitoring and data collection systems are based upon a combination of ground-based measurements, manned airborne sensors or satellite observations. These data are utilized in describing both small and large scale processes, but have spatiotemporal constraints inherent to each respective collection system. Bridging the unique spatial and temporal divides that limit current monitoring platforms is key to improving our understanding of environmental systems. In this context, Unmanned Aerial Systems (UAS) have considerable potential to radically evolve environmental monitoring. UAS-mounted sensors offer an extraordinary opportunity to bridge the existing gap between field observations and traditional air- and space-borne remote sensing, by providing not just high spatial detail over relatively large areas in a cost-effective way, but as importantly providing an entirely new capacity for enhanced temporal retrieval. As well as showcasing recent advances in the field, there is also a need to identify and understand the potential limitations of UAS technology. For these platforms to reach their monitoring potential, a wide spectrum of unresolved issues and applications specific challenges require focused community attention. Indeed, to leverage the full potential of UAS-based approaches, sensing technologies, measurement protocols, post-processing techniques, retrieval algorithms and evaluations techniques need to be harmonized. The aim of this paper is to provide a comprehensive general overview of the existing research on studies and applications of UAS in environmental monitoring in order to suggest users and researchers on future research directions, applications, developments and challenges.

Americanae nace como un proyecto conjunto que surge dentro de la Red Europea de Información y Documentación sobre América Latina (REDIAL), y que ha afrontado la Biblioteca de la Agencia Española de Cooperación Internacional para el Desarrollo (AECID). Esta nueva biblioteca virtual hace más accesibles los libros digitales de tema americanista a los investigadores y usuarios interesados de cualquier parte del mundo.