Innovations towards sustainable olive crop management: a new dawn by precision agriculture including endo-therapy.

Olive trees (Olea europaea L.) are deeply interwoven with the past, present and future of Mediterranean civilizations, both as essential economical as well as cultural valuables. Olive horticulture constitutes one of the primary agroecosystems in the Mediterranean regions of today. Being inhabitant of ecological niches, Olea europaea is prone to a peculiar vulnerability towards climatic and socioeconomical transformations that are briskly reshaping regional and global agroecosystems. Because of climatic changes and the biosafety risks of global agricultural trades, olive plants are highly susceptible to newly emerging diseases and pests, and the traditional olive horticultural crop protection practices are under scrutiny towards reducing their ecological impact. Hence there is an eminent demand for a more nature-positive olive tree crop management. Recent innovations in precision agriculture are raising the prospect for innovative crop protection methods that may provide olive farmers the required agility to respond to present and future agricultural challenges. For instance, endo-therapy, which is the systemic delivery of active ingredients via trunk injection, is a technology that holds promise of a true step-change in sustainable olive crop management. Endo-therapy allows reaching vascular diseases inaccessible to foliar treatments and delivers active ingredients in a precise manner with no risks of off-target drifts. Similarly, progresses in biological precision delivery using controlled release of active ingredients based on innovative formulation technologies are showing an exciting potential for more targeted and sustainable crop protection solutions. This review summarizes the latest innovations on both physical and biological precision deliveries in the realm of olive arboriculture in the Mediterranean regions and gives an outlook how these technologies may help orchestrating innovative olive culture practices soon.

Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi.

With >7000 species the order of rust fungi has a disproportionately large impact on agriculture, horticulture, forestry and foreign ecosystems. The infectious spores are typically dikaryotic, a feature unique to fungi in which two haploid nuclei reside in the same cell. A key example is Phakopsora pachyrhizi, the causal agent of Asian soybean rust disease, one of the world's most economically damaging agricultural diseases. Despite P. pachyrhizi's impact, the exceptional size and complexity of its genome prevented generation of an accurate genome assembly. Here, we sequence three independent P. pachyrhizi genomes and uncover a genome up to 1.25 Gb comprising two haplotypes with a transposable element (TE) content of ~93%. We study the incursion and dominant impact of these TEs on the genome and show how they have a key impact on various processes such as host range adaptation, stress responses and genetic plasticity.

Quarternary α-cyanobenzylsulfonamides: A new subclass of CAA fungicides with excellent anti-Oomycetes activity.

A bioisosteric carboxamide - sulfonamide replacement explored during the optimization of an insecticide lead compound led to the surprising discovery of a formerly unknown subclass of the Carboxylic Acid Amide (CAA) fungicides, which is the very first CAA fungicide group without a carboxamide function. In this paper we present invention pathway, racemic and stereoselective synthesis routes, structure-activity relationship studies as well as resistance profile of this novel family of fungicides.

A dispensable paralog of succinate dehydrogenase subunit C mediates standing resistance towards a subclass of SDHI fungicides in Zymoseptoria tritici.

Succinate dehydrogenase inhibitor (SDHI) fungicides are widely used for the control of a broad range of fungal diseases. This has been the most rapidly expanding fungicide group in terms of new molecules discovered and introduced for agricultural use over the past fifteen years. A particular pattern of differential sensitivity (resistance) to the stretched heterocycle amide SDHIs (SHA-SDHIs), a subclass of chemically-related SDHIs, was observed in naïve Zymoseptoria tritici populations not previously exposed to these chemicals. Subclass-specific resistance was confirmed at the enzyme level but did not correlate with the genotypes of the succinate dehydrogenase (SDH) encoding genes. Mapping and characterization of the molecular mechanisms responsible for standing SHA-SDHI resistance in natural field isolates identified a gene paralog of SDHC, termed ZtSDHC3, which encodes for an alternative C subunit of succinate dehydrogenase, named alt-SDHC. Using reverse genetics, we showed that alt-SDHC associates with the three other SDH subunits, leading to a fully functional enzyme and that a unique Qp-site residue within the alt-SDHC protein confers SHA-SDHI resistance. Enzymatic assays, computational modelling and docking simulations for the two SQR enzymes (altC-SQR, WT_SQR) enabled us to describe enzyme-inhibitor interactions at an atomistic level and to propose rational explanations for differential potency and resistance across SHA-SDHIs. European Z. tritici populations displayed a presence (20-30%) / absence polymorphism of ZtSDHC3, as well as differences in ZtSDHC3 expression levels and splicing efficiency. These polymorphisms have a strong impact on SHA-SDHI resistance phenotypes. Characterization of the ZtSDHC3 promoter in European Z. tritici populations suggests that transposon insertions are associated with the strongest resistance phenotypes. These results establish that a dispensable paralogous gene determines SHA-SDHIs fungicide resistance in natural populations of Z. tritici. This study paves the way to an increased awareness of the role of fungicidal target paralogs in resistance to fungicides and demonstrates the paramount importance of population genomics in fungicide discovery.

sRNA Profiling Combined With Gene Function Analysis Reveals a Lack of Evidence for Cross-Kingdom RNAi in the Wheat - Zymoseptoria tritici Pathosystem.

Cross-kingdom small RNA (sRNA) silencing has recently emerged as a mechanism facilitating fungal colonization and disease development. Here we characterized RNAi pathways in Zymoseptoria tritici, a major fungal pathogen of wheat, and assessed their contribution to pathogenesis. Computational analysis of fungal sRNA and host mRNA sequencing datasets was used to define the global sRNA populations in Z. tritici and predict their mRNA targets in wheat. 389 in planta-induced sRNA loci were identified. sRNAs generated from some of these loci were predicted to target wheat mRNAs including those potentially involved in pathogen defense. However, molecular approaches failed to validate targeting of selected wheat mRNAs by fungal sRNAs. Mutant strains of Z. tritici carrying deletions of genes encoding key components of RNAi such as Dicer-like (DCL) and Argonaute (AGO) proteins were generated, and virulence bioassays suggested that these are dispensable for full infection of wheat. Nonetheless, our results did suggest the existence of non-canonical DCL-independent pathway(s) for sRNA biogenesis in Z. tritici. dsRNA targeting essential fungal genes applied in vitro or generated from an RNA virus vector in planta in a procedure known as HIGS (Host-Induced Gene Silencing) was ineffective in preventing Z. tritici growth or disease. We also demonstrated that Z. tritici is incapable of dsRNA uptake. Collectively, our data suggest that RNAi approaches for gene function analyses in this fungal species and potentially also as a control measure may not be as effective as has been demonstrated for some other plant pathogenic fungi.

Hormone profiling.

Phytohormones are low molecular weight compounds that are produced by plants to regulate growth and development and also in response to biotic and abiotic stresses. The quantitative analysis of these molecules, which is essential for a better understanding of their physiological functions, is still particularly challenging due to their very low abundance in plant tissues. In this chapter, a rapid, sensitive, and accurate method for the quantification of acidic plant hormones is described. A fast and simple extraction procedure without purification or derivatization was devised, followed by optimized ultrahigh pressure liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) analysis. The analytical procedure was validated in terms of selectivity, sensitivity, linearity, precision, recovery, and matrix effects. This protocol facilitates the high-throughput analysis of the main plant hormones and is applicable as a routine tool for a wide range of research fields such as plant-pathogen interactions, mutant screening, or plant development.

Metabolomics of cereals under biotic stress: current knowledge and techniques.

Prone to attacks by pathogens and pests, plants employ intricate chemical defense mechanisms consisting of metabolic adaptations. However, many plant attackers are manipulating the host metabolism to counteract defense responses and to induce favorable nutritional conditions. Advances in analytical chemistry have allowed the generation of extensive metabolic profiles during plant-pathogen and pest interactions. Thereby, metabolic processes were found to be highly specific for given tissues, species, and plant-pathogen/pest interactions. The clusters of identified compounds not only serve as base in the quest of novel defense compounds, but also as markers for the characterization of the plants' defensive state. The latter is especially useful in agronomic applications where meaningful markers are essential for crop protection. Cereals such as maize make use of their metabolic arsenal during both local and systemic defense responses, and the chemical response is highly adapted to specific attackers. Here, we summarize highlights and recent findings of metabolic patterns of cereals under pathogen and pest attack.

Induced resistance in maize is based on organ-specific defence responses.

To obtain further insight into the intricate inter-play between maize (Zea mays) and the fungal pathogen Colletotrichum graminicola, the local and systemic molecular and chemical defence responses of maize leaves and roots were simultaneously investigated and compared. Similar gene expression and hormonal patterns were detected in both above- and below-ground organs; however, roots responded more rapidly and accumulated higher levels of defence-related hormones than leaves. Leaf and root infection with C. graminicola triggered systemic resistance in the foliage against the same fungus. This systemic defence response was associated with systemic transcriptional adaptations, and elevated levels of salicylic acid and abscisic acid. Metabolomic profiling revealed significant differences in the composition of secondary metabolites in leaves and roots, indicating that these organs employ distinct chemical defence systems. In addition, higher basal levels of antimicrobial flavonoids suggest an enhanced basal defensive state of roots. Our findings reveal tissue-specific local and systemic antifungal defence mechanisms in maize.

Small yet mighty - microRNAs in plant-microbe interactions.

Micro RNAs (miRNAs) are short non-coding RNAs of 20-24nt in length mediating RNA silencing, a eukaryotic, sequence-specific repressive gene regulation mechanism. In plants, miRNAs have a pivotal role during fundamental processes such as development, maintenance of genome integrity and abiotic stress responses. They originate from MIRNA genes that are transcribed by RNA polymerase II; MIRNA transcripts form imperfect fold-back structures that are further processed to miRNA duplexes. In Arabidopsis, over 180 MIRNA loci have been identified. Recent evidence shows that miRNAs are substantially implicated in regulating plant immunity. Pathogen attack triggers massive changes in the miRNA transcriptome; many of the altered miRNAs participate in controlling plant hormone pathways. Moreover, microorganisms are known to manipulate silencing pathways to counteract miRNA-mediated defenses. Thus far, miRNAs are believed to likely function as cardinal players in the concert of broad-spectrum disease resistance. Here, we summarize the highlights and latest findings of miRNAs as molecular regulators during plant-microbe interactions.

On the move: induced resistance in monocots.

Although plants possess an arsenal of constitutive defences such as structural barriers and preformed antimicrobial defences, many attackers are able to overcome the pre-existing defence layers. In response, a range of inducible plant defences is set up to battle these pathogens. These mechanisms, commonly integrated as induced resistance (IR), control pathogens and pests by the activation of specific defence pathways. IR mechanisms have been extensively studied in the Dicotyledoneae, whereas knowledge of IR in monocotyledonous plants, including the globally important graminaceous crop plants, is elusive. Considering the potential of IR for sustainable agriculture and the recent advances in monocot genomics and biotechnology, IR in monocots is an emerging research field. In the following, current facts and trends concerning basal immunity, and systemic acquired/induced systemic resistance in the defence of monocots against pathogens and herbivores will be summarized.

Synergies and trade-offs between insect and pathogen resistance in maize leaves and roots.

Determining links between plant defence strategies is important to understand plant evolution and to optimize crop breeding strategies. Although several examples of synergies and trade-offs between defence traits are known for plants that are under attack by multiple organisms, few studies have attempted to measure correlations of defensive strategies using specific single attackers. Such links are hard to detect in natural populations because they are inherently confounded by the evolutionary history of different ecotypes. We therefore used a range of 20 maize inbred lines with considerable differences in resistance traits to determine if correlations exist between leaf and root resistance against pathogens and insects. Aboveground resistance against insects was positively correlated with the plant's capacity to produce volatiles in response to insect attack. Resistance to herbivores and resistance to a pathogen, on the other hand, were negatively correlated. Our results also give first insights into the intraspecific variability of root volatiles release in maize and its positive correlation with leaf volatile production. We show that the breeding history of the different genotypes (dent versus flint) has influenced several defensive parameters. Taken together, our study demonstrates the importance of genetically determined synergies and trade-offs for plant resistance against insects and pathogens.