Deep‐sequencing revealed Citrus bark cracking viroid (CBCVd) as a highly aggressive pathogen on hop

Newly emerging or re‐emerging diseases are a constant and significant threat to agricultural production, so prompt and accurate identification of the causative agents is required for rapid and appropriate disease management. Classical methods of pathogen detection can be successfully supplemented by next‐generation sequencing (NGS), whereby sequence analysis can help in the discovery of new or emerging diseases. In 2007, hop growers in Slovenia reported the appearance of severely stunted hop plants, a phenomenon that spread rapidly within hop gardens and among farms. Classical diagnostic methods were unable to detect a new pathogen; therefore, single step high‐throughput parallel sequencing of total RNA and small RNAs from plants with and without symptoms was employed to identify a novel pathogen. The sequences were assembled de novo and also mapped to reference genomes, resulting in identification of a novel sequence of Citrus bark cracking viroid (CBCVd) in the stunted hop plants. Furthermore, the presence of this novel pathogen on hop was confirmed by RT‐PCR analysis of 59 plants with symptoms from 15 hop gardens, representing the main outbreak locations identified by systematic disease monitoring, and small RNA Illumina sequencing of the bulked RNA sample. The high infectivity of the newly identified CBCVd was also confirmed by biolistic inoculation of two hop cultivars, which developed aggressive symptoms in controlled conditions. This study shows the feasibility of deep sequencing for the identification of causative agents of new diseases in hop and other plants.     

Genetic diversity of Pueraria lobata (kudzu) and closely related taxa as revealed by inter-simple sequence repeat analysis

Kudzu (Pueraria lobata) is a noxious weed infesting some areas of the USA. Knowledge of its genetic variation in both native and invasive areas can lead to effective biological control measures. Inter-simple sequence repeat (ISSR) variations were studied in P. lobata and its four closely related congeneric species (P. edulis, P. montana, P. phaseoloides and P. thomsoni). ISSR results allowed a clear separation of these five species. For P. lobata, 108 plants from China and USA were analysed. The samples from the US were genetically closer to Chinese P. lobata populations than to other congeneric populations. High genetic differentiation was found for P. lobata, P. montana and P. thomsoni in Chinese samples. High genetic diversity and low population differentiation was found in P. lobata samples of the US. This supports the hypothesis of multiple introductions into the USA from different sources in Japan or China, followed by subsequent gene exchange and recombination.     

A dynamic model simulating infection of apple leaves by Venturia inaequalis

A new dynamic model of the infection of apple leaves by Venturia inaequalis is described. The model begins with the release of spores by rain and incorporates the effect of light on the discharge of ascospores from pseudothecia. The model then simulates infection through the sub-processes of germination, appressorium formation and penetration, separately for ascospores and conidia landed concurrently on wet leaves. The rate of the infection process is determined using different equations for ascospores and conidia. Spore mortality when leaves dry is determined by the stage of infection and RH in the dry period. The infection process is driven by surface wetness, temperature and RH. The progress of each infection period is measured as infection efficiency (IE), namely the percentage of landed spores which have penetrated and thereby infected leaves. The final IE quantifies the favourability of weather in each infection period. In orchard tests in each of three years, the new model detected crucial infection periods in spring and early summer which accounted for outbreaks of leaf scab. These periods were not detected by a static model based on Mills'criteria. The models performed similarly in detecting infection periods later in summer.     

Storage performance of clementines treated with hot water,sodium carbonate and sodium bicarbonate dips

Summary

The potential of using hot water (2.5 min at 45°C), 2% sodium carbonate or 2% sodium bicarbonate solutions alone or combined with hot water, for control of Penicillium digitatum (green mould) was investigated on commecially ripe clementines. The effect of such treatments on the post-harvest storage life of clementines was determined during two months analysing weight loss, increase in rind deformation and internal maturity. Carbonate and bicarbonate solutions effectively control green mould during storage but hot water does not. Compared with the control and hot-water treated fruits, clementines treated with carbonate and, to a lesser extend with bicarbonate, showed higher weight loss and lower firmness during storage. In contrast, lower increase in ripening index was found when the fruits were treated with carbonate or bicarbonate. Fruits treated with hot water alone or combined with carbonate exhibited no change in ripening during the first month of storage. Rinsing the fruit significantly reduces weight and firmness loss in the fruits treated with carbonate and bicarbonate, but did not change the ripening index. The primary finding of this work was that carbonate and bicarbonate treatments might significantly increase the loss in weight and firmness during storage. Rinsing the fruit immediately after treatment appeared to be a simple solution to avoid these losses in quality.     

Effects of shading and NO3:NH4 ratio on the yield,quality and N metabolism in strawberry

The effect of 50% shading and NO₃:NH₄ ratio (0:100, 75:25, 50:50, and 25:75) in the nutrient solution on growth, yield, quality and N metabolism in hydroponically grown strawberry (Fragaria × ananassa var Camarosa) was evaluated. Both fresh and dry weights of leaves were significantly lower when a high concentration of either NO₃ (100%) or NH₄ (75%) was the sole N source in the nutrient solution. In unshaded plants, increasing of both NH₄ and NO₃ ratio in the nutrient solution reduced photosynthetic (Pn) rate, however in shaded plants the reduction of Pn became more pronounced at a higher ratio of NH₄ in the nutrient solution. The yield in terms of fresh and dry weight of fruit per plant was significantly increased at the 75:25 and 50:50 (NO₃:NH₄) treatments. Fruit size was significantly affected by the treatments, so that the biggest fruits in both shaded and unshaded plants were obtained under the 75:25 and 50:50 (NO₃:NH₄) treatments. Total soluble solid (TSS) in unshaded plants was increased with increasing NH₄ ratio in the nutrient solution, however in shaded plants it was reduced at high NH₄ ratio in the nutrient solution. In both shaded and unshaded plants, higher concentration of NH₄ significantly reduced the post-harvest life of the fruits. The increase of tissue N concentration was nearly proportional to the NH₄ concentration in the nutrient solution. The activity of nitrate reductase (NR) was increased by increasing NH₄ from 0 to 50% and then reduced at a higher ratio of NH₄ in the solution. Shading increased NH₄ concentration so that the shaded plant had nearly twice as high NH₄ concentration in the leaves. The increase of NH₄ concentration induced by shading could be partially the reduction of NH₄ assimilate because of the shortage of carbohydrate.     

Evaluation of non-chemical seed treatment methods for the control of Alternaria dauci and A. radicina on carrot seeds

The current study was initiated to evaluate the efficacy of physical methods (hot water, aerated steam, electron treatment) and agents of natural origin (resistance inducers, plant derived products, micro-organisms) as seed treatments of carrots for control of Alternaria dauci and A. radicina. Control of both Alternaria species by seed treatment with the resistance inducers was generally poor. Results were also not satisfactory with most of the formulated commercial micro-organism preparations. Based on the average of five field trials, one of these, BA 2552 (Pseudomonas chlororaphis), provided a low but significant increase in plant stand. Among the experimental micro-organisms, the best results were obtained with Pseudomonas sp. strain MF 416 and Clonostachys rosea strain IK726. A similar level of efficacy was provided by seed treatment with an emulsion (1%) of thyme oil in water. Good and consistent control was generally achieved with the physical methods aerated steam, hot water and electron treatment. Aerated steam treatment was, apart from the thiram-containing chemical standard, the best single treatment, and its performance may at least partially be due to extensive pre-testing, resulting in dosages optimally adapted to the respective seed lot. In some of the experiments the effect of the hot water treatment, which was tested at a fixed, not specifically adapted dosage, was significantly improved when combined with a Pseudomonas sp. MF 416 or C. rosea IK726 treatment. The results are discussed in relation to the outcome of experiments in which the same seed treatment methods and agents were tested in other seed-borne vegetable pathosystems.     

Intra-specific variation and inheritance of BYDV-PAV transmission in the aphid <Emphasis Type="Italic">Sitobion avenae</Emphasis>

Vector efficiency of 44 clonal lines (clones) of Sitobion avenae belonging to 31 different genotypes (distinct patterns for five microsatellite loci) originating from Western France was evaluated by transmitting the isolate PAV4 of BYDV-PAV to barley seedlings. Variation in transmission rates from 3.7% to 92.5% was observed, with significant effects of the aphid clone, of the plant species on which clones were collected, and of the reproductive mode of the clones. When genotypes are considered instead of clones, a continuum in transmission rates was observed. A subset of S. avenae clones was tested for transmission of one (10 clones) and 13 (4 clones) other BYDV-PAV isolates, and a clear clone effect modulated by an isolate effect was observed. Crosses were made between clones with different vectoring phenotypes and their F1 progeny were tested for PAV4 transmission. The narrow sense heritability of the PAV transmission character was rather high in the F1 families (h²=0.5) and the segregation analyses suggested an oligo/polygenic determinism of this character. The possibility of generating new transmission variants by sexual reproduction and its consequences on transmission mechanism studies and on BYD epidemics are discussed.     

A DNA-based evaluation of North American river otter diet with respect to fishes: Implications for the conservation of aquatic predators and their prey

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