Diversity, migration routes, and worldwide population genetic structure of Lecanosticta acicola, the causal agent of brown spot needle blight.

Lecanosticta acicola is a pine needle pathogen causing brown spot needle blight that results in premature needle shedding with considerable damage described in North America, Europe, and Asia. Microsatellite and mating type markers were used to study the population genetics, migration history, and reproduction mode of the pathogen, based on a collection of 650 isolates from 27 countries and 26 hosts across the range of L. acicola. The presence of L. acicola in Georgia was confirmed in this study. Migration analyses indicate there have been several introduction events from North America into Europe. However, some of the source populations still appear to remain unknown. The populations in Croatia and western Asia appear to originate from genetically similar populations in North America. Intercontinental movement of the pathogen was reflected in an identical haplotype occurring on two continents, in North America (Canada) and Europe (Germany). Several shared haplotypes between European populations further suggests more local pathogen movement between countries. Moreover, migration analyses indicate that the populations in northern Europe originate from more established populations in central Europe. Overall, the highest genetic diversity was observed in south-eastern USA. In Europe, the highest diversity was observed in France, where the presence of both known pathogen lineages was recorded. Less than half of the observed populations contained mating types in equal proportions. Although there is evidence of some sexual reproduction taking place, the pathogen spreads predominantly asexually and through anthropogenic activity.

Novel Insights Into Refugia at the Southern Margin of the Distribution Range of the Endangered Species Ulmus laevis.

Riparian ecosystems, in long-time developed regions, are among the most heavily impacted by human activities; therefore, the distribution of tree riparian species, such as Ulmus laevis, is highly affected. This phenomenon is particularly relevant at the margins of the natural habitat of the species, where populations are small and rare. In these cases, it is difficult to distinguish between relics or introductions, but it is relevant for the restoration of natural habitats and conservation strategies. The aim of this study was to study the phylogeography of the southern distribution of the species. We sequenced the entire chloroplast (cp) genomes of 54 individuals from five sampled populations across different European regions to highlight polymorphisms and analyze their distribution. Thirty-two haplotypes were identified. All the sampled populations showed private haplotypes that can be considered an indicator of long-term residency, given the low mutation rate of organellar DNA. The network of all haplotypes showed a star-like topology, and Serbian haplotypes were present in all branches. The Balkan population showed the highest level of nucleotide and genetic diversity. Low genetic differentiation between populations was observed but we found a significant differentiation among Serbia vs. other provenances. Our estimates of divergent time of U. laevis samples highlight the early split of above all Serbian individuals from other populations, emphasizing the reservoir role of white elm genetic diversity of Serbian population.

Worldwide Genetic Structure Elucidates the Eurasian Origin and Invasion Pathways of Dothistroma septosporum, Causal Agent of Dothistroma Needle Blight.

Dothistroma septosporum, the primary causal agent of Dothistroma needle blight, is one of the most significant foliar pathogens of pine worldwide. Its wide host and environmental ranges have led to its global success as a pathogen and severe economic damage to pine forests in many regions. This comprehensive global population study elucidated the historical migration pathways of the pathogen to reveal the Eurasian origin of the fungus. When over 3800 isolates were examined, three major population clusters were revealed: North America, Western Europe, and Eastern Europe, with distinct subclusters in the highly diverse Eastern European cluster. Modeling of historical scenarios using approximate Bayesian computation revealed the North American cluster was derived from an ancestral population in Eurasia. The Northeastern European subcluster was shown to be ancestral to all other European clusters and subclusters. The Turkish subcluster diverged first, followed by the Central European subcluster, then the Western European cluster, which has subsequently spread to much of the Southern Hemisphere. All clusters and subclusters contained both mating-types of the fungus, indicating the potential for sexual reproduction, although asexual reproduction remained the primary mode of reproduction. The study strongly suggests the native range of D. septosporum to be in Eastern Europe (i.e., the Baltic and Western Russia) and Western Asia.

Thousand cankers disease in Juglans: Optimizing sampling and identification procedures for the vector Pityophthorus juglandis, and the causal agent Geosmithia morbida.

Lindgren funnel traps were used to monitor Pityophthorus juglandis occurrence. Traps were placed directly on walnut trees, with the top tied to one of the lower branches (about 2m high). An 8-funnel model was used instead of a 4-funnel trap, with the specific pheromone bait positioned between the fourth and the fifth funnel. Traps were customized with a 5mm metal mesh which was placed inside the bottom funnel so that debris (mainly foliage) and larger non-target insects would not end up inside the collecting jar. Geosmithia morbida was isolated from beetle adults, larvae and necrotic woody tissue around beetle galleries. Contaminant-free colonies were subcultured in purity and identified by: a) colony phenotyping [morphology, texture and pigmentation; margin type (regular/irregular; lobed/non-lobed); mycelium compactness; surface bumpiness; growth/temperature relationships]; b) micromorphology: type, morphology and ontogeny of conidiophores, metulae and phialides; conidiogenesis; shape, dimension and pigmentation of conidia; c) DNA fingerprinting.•Our protocol was customized to prevent traps from swinging in the wind and to optimize beetle catches by transversely fixing the bottom of funnel traps to the tree trunk with wooden shafts for stability.•To enhance fungus isolation in purity, a semi-selective Potato Dextrose Agar (PDA) medium, enriched with the antibiotics Ampicillin (Policillin-N) and Rifampicin (Rifamycin), was devised to prevent contamination by Gram-positive and Gram-negative bacteria and by mycobacteria.

Transferability of PCR-based diagnostic protocols: An international collaborative case study assessing protocols targeting the quarantine pine pathogen Fusarium circinatum.

Fusarium circinatum is a harmful pathogenic fungus mostly attacking Pinus species and also Pseudotsuga menziesii, causing cankers in trees of all ages, damping-off in seedlings, and mortality in cuttings and mother plants for clonal production. This fungus is listed as a quarantine pest in several parts of the world and the trade of potentially contaminated pine material such as cuttings, seedlings or seeds is restricted in order to prevent its spread to disease-free areas. Inspection of plant material often relies on DNA testing and several conventional or real-time PCR based tests targeting F. circinatum are available in the literature. In this work, an international collaborative study joined 23 partners to assess the transferability and the performance of nine molecular protocols, using a wide panel of DNA from 71 representative strains of F. circinatum and related Fusarium species. Diagnostic sensitivity, specificity and accuracy of the nine protocols all reached values >80%, and the diagnostic specificity was the only parameter differing significantly between protocols. The rates of false positives and of false negatives were computed and only the false positive rates differed significantly, ranging from 3.0% to 17.3%. The difference between protocols for some of the performance values were mainly due to cross-reactions with DNA from non-target species, which were either not tested or documented in the original articles. Considering that participating laboratories were free to use their own reagents and equipment, this study demonstrated that the diagnostic protocols for F. circinatum were not easily transferable to end-users. More generally, our results suggest that the use of protocols using conventional or real-time PCR outside their initial development and validation conditions should require careful characterization of the performance data prior to use under modified conditions (i.e. reagents and equipment). Suggestions to improve the transfer are proposed.

Geosmithia-Ophiostoma: a New Fungus-Fungus Association.

In Europe as in North America, elms are devastated by Dutch elm disease (DED), caused by the alien ascomycete Ophiostoma novo-ulmi. Pathogen dispersal and transmission are ensured by local species of bark beetles, which established a novel association with the fungus. Elm bark beetles also transport the Geosmithia fungi genus that is found in scolytids' galleries colonized by O. novo-ulmi. Widespread horizontal gene transfer between O. novo-ulmi and Geosmithia was recently observed. In order to define the relation between these two fungi in the DED pathosystem, O. novo-ulmi and Geosmithia species from elm, including a GFP-tagged strain, were grown in dual culture and mycelial interactions were observed by light and fluorescence microscopy. Growth and sporulation of O. novo-ulmi in the absence or presence of Geosmithia were compared. The impact of Geosmithia on DED severity was tested in vivo by co-inoculating Geosmithia and O. novo-ulmi in elms. A close and stable relation was observed between the two fungi, which may be classified as mycoparasitism by Geosmithia on O. novo-ulmi. These results prove the existence of a new component in the complex of organisms involved in DED, which might be capable of reducing the disease impact.

Correction to: Geosmithia-Ophiostoma: a New Fungus-Fungus Association.

The article Geosmithia-Ophiostoma: a New Fungus-Fungus Association, written by Alessia L. Pepori, Priscilla P. Bettini, Cecilia Comparini, Sabrina Sarrocco, Anna Bonini, Arcangela Frascella, Luisa Ghelardini, & Aniello Scala, Giovanni Vannacci, Alberto Santini.

Genetic architecture of spring and autumn phenology in Salix.

BACKGROUND: In woody plants from temperate regions, adaptation to the local climate results in annual cycles of growth and dormancy, and optimal regulation of these cycles are critical for growth, long-term survival, and competitive success. In this study we have investigated the genetic background to growth phenology in a Salix pedigree by assessing genetic and phenotypic variation in growth cessation, leaf senescence and bud burst in different years and environments. A previously constructed linkage map using the same pedigree and anchored to the annotated genome of P. trichocarpa was improved in target regions and used for QTL analysis of the traits. The major aims in this study were to map QTLs for phenology traits in Salix, and to identify candidate genes in QTL hot spots through comparative mapping with the closely related Populus trichocarpa. RESULTS: All traits varied significantly among genotypes and the broad-sense heritabilities ranged between 0.5 and 0.9, with the highest for leaf senescence. In total across experiment and years, 80 QTLs were detected. For individual traits, the QTLs explained together from 21.5 to 56.5% of the variation. Generally each individual QTL explained a low amount of the variation but three QTLs explained above 15% of the variation with one QTL for leaf senescence explaining 34% of the variation. The majority of the QTLs were recurrently identified across traits, years and environments. Two hotspots were identified on linkage group (LG) II and X where narrow QTLs for all traits co-localized. CONCLUSIONS: This study provides the most detailed analysis of QTL detection for phenology in Salix conducted so far. Several hotspot regions were found where QTLs for different traits and QTLs for the same trait but identified during different years co-localised. Many QTLs co-localised with QTLs found in poplar for similar traits that could indicate common pathways for these traits in Salicaceae. This study is an important first step in identifying QTLs and candidate genes for phenology traits in Salix.

Rapid detection of Ceratocystis platani inoculum by quantitative real-time PCR assay.

Ceratocystis platani is the causal agent of canker stain of plane trees, a lethal disease able to kill mature trees in one or two successive growing seasons. The pathogen is a quarantine organism and has a negative impact on anthropogenic and natural populations of plane trees. Contaminated sawdust produced during pruning and sanitation fellings can contribute to disease spread. The goal of this study was to design a rapid, real-time quantitative PCR assay to detect a C. platani airborne inoculum. Airborne inoculum traps (AITs) were placed in an urban setting in the city of Florence, Italy, where the disease was present. Primers and TaqMan minor groove binder (MGB) probes were designed to target cerato-platanin (CP) and internal transcribed spacer 2 (ITS2) genes. The detection limits of the assay were 0.05 pg/µl and 2 fg/µl of fungal DNA for CP and ITS, respectively. Pathogen detection directly from AITs demonstrated specificity and high sensitivity for C. platani, detecting DNA concentrations as low as 1.2 × 10(-2) to 1.4 × 10(-2) pg/µl, corresponding to ∼10 conidia per ml. Airborne inoculum traps were able to detect the C. platani inoculum within 200 m of the closest symptomatic infected plane tree. The combination of airborne trapping and real-time quantitative PCR assay provides a rapid and sensitive method for the specific detection of a C. platani inoculum. This technique may be used to identify the period of highest risk of pathogen spread in a site, thus helping disease management.

Optimizing nitrogen economy under drought: increased leaf nitrogen is an acclimation to water stress in willow (Salix spp.).

BACKGROUND AND AIMS: The major objective was to identify plant traits functionally important for optimization of shoot growth and nitrogen (N) economy under drought. Although increased leaf N content (area basis) has been observed in dry environments and theory predicts increased leaf N to be an acclimation to drought, experimental evidence for the prediction is rare. METHODS: A pedigree of 200 full-sibling hybrid willows was pot-grown in a glasshouse in three replicate blocks and exposed to two water regimes for 3 weeks. Drought conditions were simulated as repeated periods of water shortage. The total leaf mass and area, leaf area efficiency (shoot growth per unit leaf area, E(A)), area-based leaf N content (N(A)), total leaf N pool (N(L)) and leaf N efficiency (shoot growth per unit leaf N, E(N)) were assessed. KEY RESULTS: In the water-stress treatment, shoot biomass growth was N limited in the genotypes with low N(L), but increasingly limited by other factors in the genotypes with greatest N(L). The N(A) was increased by drought, and drought-induced shift in N(A) varied between genotypes (significant G × E). Judged from the E(A)-N(A) relationship, optimal N(A) was 16 % higher in the water-stress compared with the well-watered treatment. Biomass allocation to leaves and shoots varied between treatments, but the treatment response of the leaf : shoot ratio was similar across all genotypes. CONCLUSIONS: It is concluded that N-uptake efficiency and leaf N efficiency are important traits to improve growth under drought. Increased leaf N content (area basis) is an acclimation to optimize N economy under drought. The leaf N content is an interesting trait for breeding of willow bioenergy crops in a climate change future. In contrast, leaf biomass allocation is a less interesting breeding target to improve yield under drought.

Bud dormancy release in elm (Ulmus spp.) clones--a case study of photoperiod and temperature responses.

Dormancy release as influenced by duration of outdoor winter chilling in Florence (Italy) was studied under different photoperiodic and temperature treatments in collected twigs of two European (Ulmus glabra Huds. and Ulmus minor Mill.) and four Asian (Ulmus pumila L., Ulmus parvifolia Jacq., Ulmus macrocarpa Hance and Ulmus villosa Brandis) elm clones. Photoperiod had no effect on dormancy release, and there was no evidence that photoperiod affected bud burst during quiescence in the studied elm clones. Thermal time (day degrees >0 degrees C) to bud burst decreased in all the clones with increasing outdoor chilling. Although all the clones exhibited a rather weak dormancy, they significantly differed from each other. Dormancy was released earlier in the Asian than in the European clones, and the clones could be ranked from the U. pumila clone (very weak and short dormancy) to the U. minor clone (relatively stronger and longer dormancy), the other clones being intermediate. In all the clones except U. minor, the observed decrement in thermal time to bud burst was efficiently explained as an inverse exponential function of the number of chill days < or =5 degrees C received outdoor in autumn and winter. Endodormancy, as measured by the single-node cuttings test, was weak and short in all the clones. The latter result suggests that correlative inhibitions were largely responsible for preventing bud burst during winter in these elm clones.