A robust hydroponic-based system for screening red clover (Trifolium pratense) for Fusarium avenaceum

Red clover (Trifolium pratense) is an important forage legume crop that suffers likemost perennial crops from attacks by soil-borne pathogens.Fusariumroot rot is oneof the most serious diseases and at the same time problematic to identify resistancebecause of its hidden life in the soil. Current screening methods are laborious andhampered by limited reproducibility. To remedy this situation, we aimed to establisha simple and reliable hydroponics-based screening system to facilitate studies of redclover–Fusarium avenaceuminteractions. First, the fungal spore concentrations werebalanced toward the development of red clover plants grown hydroponically. Wefound that the optimum concentration was 30,000 spores in 2 L of hydroponicmedium to ensure infection during the plant growth period in this system. The proce-dure was scaled-up to screen plants from 25 populations to identify red clover indi-viduals with the improved resistance toF. avenaceum. Susceptible plants hadapproximately two-fold higher amounts of fungal DNA than resistant plants, demon-strating a correlation between the disease readings of the plants and pathogen DNA.We foresee this screening procedure meeting the needs of both applied breedingwork and in-depth molecular studies of responses between this pathogen and itshost plant. This method could be applied for the screening of other plant species forresistance toFusariumspp. or to other root microbes

Dynamics of nucleic acid mobility

Advances in sequencing technologies and bioinformatic analyses are accelerating the quantity and quality of data from all domains of life. This rich resource has the potential to reveal a number of important incidences with respect to possible exchange of nucleic acids. Ancient events have impacted species evolution and adaptation to new ecological niches. However, we still lack a full picture of processes ongoing within and between somatic cells, gametes, and different organisms. We propose that events linked to acceptance of alien nucleic acids grossly could be divided into 2 main routes in plants: one, when plants are exposed to extreme challenges and, the second level, a more everyday or season-related stress incited by biotic or abiotic factors. Here, many events seem to comprise somatic cells. Are the transport and acceptance processes of alien sequences random or are there specific regulatory systems not yet fully understood? Following entrance into a new cell, a number of intracellular processes leading to chromosomal integration and function are required. Modification of nucleic acids and possibly exchange of sequences within a cell may also occur. Such fine-tune events are most likely very common. There are multiple questions that we will discuss concerning different types of vesicles and their roles in nucleic acid transport and possible intracellular sequence exchange between species

Red clover root-associated microbiota is shaped by geographic location and choice of farming system

Aims: This study evaluated the red clover (Trifolium pratense) root-associated microbiota to clarify the presence of pathogenic and beneficial microorganisms in 89 Swedish field sites.Methods and results: 16S rRNA and ITS amplicon sequencing analysis were performed on DNA extracted from the red clover root samples collected to determine the composition of the prokaryotic and eukaryotic root-associated microbe communities. Alpha and beta diversities were calculated and relative abundance of various microbial taxa and their co-occurrence were analyzed. Rhizobium was the most prevalent bacterial genus, followed by Sphingomonas, Mucilaginibacter, Flavobacterium, and the unclassified Chloroflexi group KD4-96. The Leptodontidium, Cladosporium, Clonostachys, and Tetracladium fungal genera known for endophytic, saprotrophic, and mycoparasitic lifestyles were also frequently observed in all samples. Sixty-two potential pathogenic fungi were identified with a bias toward grass pathogens and a higher abundance in samples from conventional farms.Conclusions: We showed that the microbial community was mainly shaped by geographic location and management procedures. Co-occurrence networks revealed that the Rhizobiumleguminosarum bv. trifolii was negatively associated with all fungal pathogenic taxa recognized in this study

Fragmentation of tRNA in Phytophthora infestans asexual life cycle stages and during host plant infection

The oomycete Phytophthora infestans possesses active RNA silencing pathways, which presumably enable this plant pathogen to control the large numbers of transposable elements present in its 240 Mb genome. Small RNAs (sRNAs), central molecules in RNA silencing, are known to also play key roles in this organism, notably in regulation of critical effector genes needed for infection of its potato host.Results: To identify additional classes of sRNAs in oomycetes, we mapped deep sequencing reads to transfer RNAs (tRNAs) thereby revealing the presence of 19-40 nt tRNA-derived RNA fragments (tRFs). Northern blot analysis identified abundant tRFs corresponding to half tRNA molecules. Some tRFs accumulated differentially during infection, as seen by examining sRNAs sequenced from P. infestans-potato interaction libraries. The putative connection between tRF biogenesis and the canonical RNA silencing pathways was investigated by employing hairpin RNA-mediated RNAi to silence the genes encoding P. infestans Argonaute (PiAgo) and Dicer (PiDcl) endoribonucleases. By sRNA sequencing we show that tRF accumulation is PiDcl1-independent, while Northern hybridizations detected reduced levels of specific tRNA-derived species in the PiAgo1 knockdown line.Conclusions: Our findings extend the sRNA diversity in oomycetes to include fragments derived from non-protein-coding RNA transcripts and identify tRFs with elevated levels during infection of potato by P. infestans

Plant host range of Verticillium longisporum and microsclerotia density in Swedisch soils

Verticillium longisporum is a soil-borne fungal pathogen causing vascular wilt of Brassica crops. This study was conducted to enhance our knowledge on the host range of V. longisporum. Seven crop species (barley, oat, oilseed rape, pea, red clover, sugar beet and wheat) and five weed species (barren brome, black-grass, charlock, cleavers and scentless mayweed) all common in southern Sweden were evaluated for infection by response to V. longisporum. Oat, spring wheat, oilseed rape, scentless mayweed and charlock inoculated with V. longisporum in a greenhouse showed stunting to various degrees close to the fully ripe stage. Based on the extent of microsclerotia formation, explants were separated into four groups: for pea and wheat, 80%. The results suggest that plant species outside the Brassicaceae can act as reservoirs of V. longisporum inoculum. Soil inoculum densities in nine fields were monitored over a period of 12 months, which ranged from 1 to 48 cfu g¿1 soil. Density of microsclerotia was lowest just after harvest, reaching its maximum six months later. No significant correlation between inoculum density in soil and disease incidence on oilseed rape plants was found. However, the data suggest that a threshold of 1 cfu g¿1 soil is needed to cause disease on oilseed rape. Species identification based on microsclerotia morphology and PCR analysis showed that V. longisporum dominated in soil of seven, and V. dahliae in two of the nine fields studied

The Euroscapes network

-Sustainable landscapes require evidence-based knowledge about multiple goods, services and values, as well as integrated place-based collaboration among actors and stakeholders at multiple levels. -EUROSCAPES is an international network of researchers, journalists and practitioners that supports sharing of knowledge about how to maintain and develop sustainable landscapes. --Euro... is about the diversity of places in the European continent’s East and West - from the Ural Mountains and Caucasus to the Atlantic Ocean. --...scapes links to the word landscape, which has biophysical, anthropogenic and perceived dimensions. -EUROSCAPES gathers and communicates knowledge using three series of publications: --EUROSCAPES News with short texts and illustrations that can be used by journalists. --EUROSCAPES Communication with popular summaries of peer-reviewed publications and reports. --EUROSCAPES Report with longer peer-reviewed comprehensive text. -EUROSCAPES uses the web site www.euroscapes.org to disseminate these publication series using five themes: People, Places, Practices, Projects, and Publications

DYNAMICS OF Cercospora zeina POPULATIONS IN MAIZE-BASED AGRO-ECOLOGIES OF UGANDA

Stability of pathogen populations characterised by slow temporal variation is important for durability of disease management systems in any agroecology. Temporal variation in population structure is attributed to factors related to ecology, biology and life history, and varies among organisms and ecosystems. The objective of this study was to investigate genetic variability of Cercospora zeina (previously called Cercospora zeae-maydis Type II) populations in maize ( Zea mays ) producing areas under Uganda conditions. Populations of the fungus were analysed for genetic variability using a fluorescent amplified fragment length polymorphism (AFLP) technique. Little or no genetic differentiation (\u3a6FST 0.05) was detected for populations sampled within the same year, within an agroecology. However, a weak to moderate population structure was detected between populations from different locations, within the same (\u3a6FST = 0.08) or different agroecologies (\u3a6FST = 0.09). Pair-wise comparisons using \u3a6FST gene diversity and genetic distance, showed a reduction in genetic diversity in younger populations, suggestive of minor effects of selection and genetic drift. Overall, the data suggest that during the 3 years of study the impact of selection and genetic drift on C. zeina populations in the two Ugandan agroecologies is slow, but progressive leading to homogenetity with agroecologies and differences between agroecologies.La stabilit\ue9 des populations d\u2019agents pathog\ue8nes caract\ue9ris\ue9e par une faible variation dans le temps, est importante pour la durabilit\ue9 dans les syst\ue8mes de gestion des pathologies des plantes dans n\u2019importe quelle zone agro-\ue9cologique. La variation dans le temps au sein d\u2019une population, est fonction de facteurs relatifs \ue0 l\u2019\ue9cologie, la biologie et l\u2019histoire de vie des pathog\ue8nes. Elle varie d\u2019un \ueatre vivant \ue0 un autre et d\u2019un \ue9cosyst\ue8me \ue0 un autre. L\u2019objectif de cette \ue9tude \ue9tait d\u2019\ue9valuer la variabilit\ue9 g\ue9n\ue9tique au sein des populations de Cercospora zeina (pr\ue9cedemment appel\ue9 Cercospora zeae-maydis Type II) dans les zones productrice de ma\uefs ( Zea mays ) en Ouganda. Les populations de ce champignon microscopique ont \ue9t\ue9 soumises \ue0 une \ue9tude de variabilit\ue9 g\ue9n\ue9tique gr\ue2ce \ue0 la technique du polymorphisme de longueur de fragments amplifi\ue9s (AFLP). Tr\ue8s peu ou aucune variation g\ue9n\ue9tique (\u3a6FST 0.05) n\u2019a \ue9t\ue9 observ\ue9e pour les populations \ue9chantillonn\ue9es au cours de la m\ueame ann\ue9e, dans une zone agro-\ue9cologique donn\ue9e. N\ue9anmoins, une structure populationnelle d\u2019envergure faible \ue0 mod\ue9r\ue9e a \ue9t\ue9 observ\ue9e entre les populations de diff\ue9rentes origines, (\u3a6FST = 0.08) \ue0 l\u2019int\ue9rieur d\u2019une m\ueame population ou (\u3a6FST = 0.09) entre les populations de diff\ue9rente zones agro \ue9cologique. La comparaison par paires utilisant \u3a6FST diversit\ue9 des g\ue8nes et distance g\ue9n\ue9tique, a montr\ue9 une r\ue9duction de diversit\ue9 g\ue9n\ue9tique dans les populations les plus jeunes, sugg\ue9rant ainsi un effet mineur de s\ue9lection et de d\ue9rive g\ue9n\ue9tique. Au total, les donn\ue9es collect\ue9es indiquent un faible impact de s\ue9lection et de d\ue9rive g\ue9n\ue9tique sur les populations de C. zeina dans les deux zones agro-\ue9cologiques Ougandaise durant les 3 ann\ue9es de l\u2019\ue9tude, mais cet impact est progressif et responsable de l\u2019homog\ue9n\ue9it\ue9 au sein des zones agro-\ue9cologiques et des diff\ue9rences entre les zones agro-\ue9cologiques

A calibration method for non-overlapping cameras based on mirrored phase target

A novel calibration method for non-overlapping cameras is proposed in this paper. A LCD screen is used as a phase target to display two groups of orthogonal phase-shifted sinusoidal patterns during the calibration process. Through a mirror reflection, the phase target is captured by the cameras respectively. The relations between each camera and the phase target can be obtained according the proposed algorithm. Then the relation between the cameras can be calculated by treating the phase target as an intermediate value. The proposed method is more flexible than conventional mirror-based approach, because it do not require the common identification points and is robust to out-of-focus images. Both simulation work and experimental results show the proposed calibration method has a good result in calibrating a non-overlapping cameras system

Stop worrying; start growing: Risk research on GM crops is a dead parrot: it is time to start reaping the benefits of GM

Opponents of genetically modified crops continue to raise concerns about risk, despite 20 years of research disproving their claims. Science should close the book on risk research and turn to studying the economic and environmental benefits of agricultural biotechnolog