Verticillium wilt resistant and susceptible olive cultivars express a very different basal set of genes in roots

Characterization of the Metabolic Profile of Olive Tissues (Roots, Stems and Leaves): Relationship with Cultivars' Resistance/Susceptibility to the Soil Fungus Verticillium dahliae

Verticillium wilt of olive (VWO) is one of the most widespread and devastating olive diseases in the world. Harnessing host resistance to the causative agent is considered one of the most important measures within an integrated control strategy of the disease. Aiming to understand the mechanisms underlying olive resistance to VWO, the metabolic profiles of olive leaves, stems and roots from 10 different cultivars with varying levels of susceptibility to this disease were investigated by liquid chromatography coupled to mass spectrometry (LC-MS). The distribution of 56 metabolites among the three olive tissues was quantitatively assessed and the possible relationship between the tissues' metabolic profiles and resistance to VWO was evaluated by applying unsupervised and supervised multivariate analysis. Principal component analysis (PCA) was used to explore the data, and separate clustering of highly resistant and extremely susceptible cultivars was observed. Moreover, partial least squares discriminant analysis (PLS-DA) models were built to differentiate samples of highly resistant, intermediate susceptible/resistant, and extremely susceptible cultivars. Root models showed the lowest classification capability, but metabolites from leaf and stem were able to satisfactorily discriminate samples according to the level of susceptibility. Some typical compositional patterns of highly resistant and extremely susceptible cultivars were described, and some potential resistance/susceptibility metabolic markers were pointed out.

OliveAtlas: A Gene Expression Atlas Tool for Olea europaea

The olive (Olea europaea L.) is an ancient crop of great importance in the Mediterranean basin due to the production of olive oil and table olives, which are important sources of fat and have benefits for human health. This crop is expanding and increasing its production worldwide and five olive genomes have recently been sequenced, representing a wild olive and important cultivars in terms of olive oil production, intensive agriculture, and adaptation to the East Asian climate. However, few bioinformatic and genomic resources are available to assist olive research and breeding, and there are no platforms to query olive gene expression data. Here, we present OliveAtlas, an interactive gene expression atlas for olive with multiple bioinformatics tools and visualization methods, enabling multiple gene comparison, replicate inspection, gene set enrichment, and data downloading. It contains 70 RNA-seq experiments, organized in 10 data sets representing the main olive plant organs, the pollen germination and pollen tube elongation process, and the response to a collection of biotic and abiotic stresses, among other experimental conditions. OliveAtlas is a web tool based on easyGDB with expression data based on the 'Picual' genome reference and gene annotation.

Avoidant/resistant rather than tolerant olive rootstocks are more effective in controlling Verticillium wilt

The identification of rootstocks of low susceptibility to Verticillium dahliae can become a valuable procedure to achieve effective control of Verticillium wilt in the olive grove. This not only involves the identification of suitable genotypes, but also the study of the interaction between the rootstock and the grafted scion. Thus, a rootstock that prevents or minimizes V. dahliae proliferation (avoidance/resistance strategy) can have very different effects on a susceptible scion compared to a rootstock that shows few or no symptoms despite being infected (tolerance strategy). Both resistance and tolerance mechanisms have been recently identified in wild olive genotypes with low susceptibility to V. dahliae. When used as rootstocks of the highly susceptible variety 'Picual', we found that resistant genotypes, including the cultivar 'Frantoio', were more effective than tolerant genotypes in controlling Verticillium wilt. Furthermore, tolerant genotypes were as ineffective as susceptible or extremely susceptible genotypes in controlling Verticillium wilt. We also identified rootstock-scion combinations with behaviours that were not expected according to the degree of susceptibility previously observed in the non-grafted rootstock. Although the rootstocks were able to control Verticillium wilt according to its degree of susceptibility to V. dahliae, the ability to control the infection was not adequately transferred to the grafted scion. Our results confirmed that: the degree of susceptibility to Verticillium wilt of an olive variety does not predict its performance as a rootstock; to use a very low susceptible genotype as rootstock of a susceptible scion increases the susceptibility of the genotype used as rootstock; in any case, avoidant/resistant rootstocks are more effective than tolerant rootstocks in reducing the susceptibility of the grafted plant to V. dahliae.

Unveiling Differences in Root Defense Mechanisms Between Tolerant and Susceptible Olive Cultivars to Verticillium dahliae

Verticillium wilt of olive (VWO), caused by the soil-borne vascular pathogen Verticillium dahliae, is one of the most devastating diseases affecting olive, the woody crop. One of the best VWO management measures is the use of tolerant cultivars. Yet, our knowledge about defense mechanisms that operate at the root level to explain tolerance to this disease is incomplete. Moreover, most of the approaches so far followed focus only on a specific mechanistic level (e.g., genetic, physiological, or biochemical) rather than on a holistic/multilevel perspective. In this study, eighteen root functional traits, the time-course expression of nine defense-related genes, the root lignin content, and the root membrane permeability were evaluated in six olive varieties differing in their level of tolerance/susceptibility to VWO. The aim was to find links between the level of tolerance to VWO and specific root defense mechanisms at the structural, genetic, biochemical, and physiological levels. Tolerant and susceptible cultivars showed substantial differences in the root system architecture and root lignin content. VWO-susceptible cultivars presented roots with higher specific length and area, but lower diameter and larger number of forks and tips compared to tolerant varieties that also showed less branched roots, higher root diameter, and larger basal content of lignin. Interestingly, VWO-tolerant varieties significantly increased their root lignin content and root membrane permeability after inoculation with V. dahliae. These results were seldom (or not at all) observed in the susceptible plants. At the genetic level, genes related to defense mechanisms, such as cell wall lignin biosynthesis (C4H and CO-MT), production of hydrolytic enzymes able to degrade the fungal cell wall (β-1.3-glucanase), and activation of innate immunity (BAK1 and WRKY5) increased their expression in tolerant cultivars from early moments after inoculation, in contrast to the susceptible ones. These results showed that differences in the root system architecture and lignin content may greatly determine the performance of olive against colonization and invasion by V. dahliae. Moreover, the increase in root membrane permeability in the presence of the pathogen was a typical response of tolerant cultivars. Finally, VWO-tolerant cultivars were able to mount a more intense and rapid defense-related genetic response to respond to the attack by V. dahliae.

Olive Oil Sensory Analysis as a Tool to Preserve and Valorize the Heritage of Centenarian Olive Trees

In inland areas of Portugal and some regions of the Mediterranean basin, olive production is based on traditional olive groves, with low intensification, local cultivars, aged plants, and centenarian trees. These plants play a key role in the ecosystem, contributing to carbon sequestration and possessing a high genetic diversity, particularly important for selecting cultivars more resistant to climatic changes. Appreciation of the value of this genetic diversity implies genetic, morphological, and physicochemical characterization of centenarian trees, which is expensive and time-consuming. Sensory evaluation is also of utmost importance. Thus, in this study, centenarian olive trees were selected in the Côa Valley region, a UNESCO World Heritage site. The descriptive sensory profile of their extracted olive oils was established and used to cluster the oils, using hierarchical clustering analysis, and consequently the olive trees, into five groups with similar intensities of perceived olfactory-gustatory attributes. Each cluster revealed olive oils with unique sensory patterns, presumably due to similarities of the olive trees, confirming the potential of the proposed screening approach. The identification of sensorially homogeneous oil-tree groups would reduce the number of specimens needed for subsequent morphological, genetic, and chemical characterization, allowing a cost-effective and robust future evaluation procedure.

Coupling the endophytic microbiome with the host transcriptome in olive roots

The connection between olive genetic responses to environmental and agro-climatic conditions and the composition, structure and functioning of host-associated, belowground microbiota has never been studied under the holobiont conceptual framework. Two groups of cultivars growing under the same environmental, pedological and agronomic conditions, and showing highest (AH) and lowest (AL) Actinophytocola relative abundances, were earlier identified. We aimed now to: i) compare the root transcriptome profiles of these two groups harboring significantly different relative abundances in the above-mentioned bacterial genus; ii) examine their rhizosphere and root-endosphere microbiota co-occurrence networks; and iii) connect the root host transcriptome pattern to the composition of the root microbial communities by correlation and co-occurrence network analyses. Significant differences in olive gene expression were found between the two groups. Co-occurrence networks of the root endosphere microbiota were clearly different as well. Pearson's correlation analysis enabled a first portray of the interaction occurring between the root host transcriptome and the endophytic community. To further identify keystone operational taxonomic units (OTUs) and genes, subsequent co-occurrence network analysis showed significant interactions between 32 differentially expressed genes (DEGs) and 19 OTUs. Overall, negative correlation was detected between all upregulated genes in the AH group and all OTUs except of Actinophytocola. While two groups of olive cultivars grown under the same conditions showed significantly different microbial profiles, the most remarkable finding was to unveil a strong correlation between these profiles and the differential gene expression pattern of each group. In conclusion, this study shows a holistic view of the plant-microbiome communication.

Functional Traits of Olive Varieties and Their Relationship with the Tolerance Level towards Verticillium Wilt

Verticillium wilt of olive (VWO), caused by the soil-borne pathogen Verticillium dahliae, is considered one of the most important diseases affecting this tree crop. One of the best VWO management measures is the use of tolerant cultivars. Remarkably, no information is available about olive functional traits and their potential relationship with tolerance to V. dahliae. Twenty-five selected functional traits (for leaf, stem, root and whole plant) were evaluated in six olive varieties differing in their VWO tolerance level to identify possible links between this phenotype and functional traits’ variation. High intervarietal diversity was found among cultivars and several functional traits were related with VWO tolerance. Tolerant varieties showed higher leaf area, dry matter content (leaf, stem and plant) and mass fraction for stems, but lower for leaves. Significant differences were also detected for root functional traits, tolerant cultivars displaying larger fine root diameter and lignin content but smaller specific length and area of thick and fine roots. Correlations were found among functional traits both within varieties and between levels of tolerance/susceptibility to VWO. Associations were observed between biomass allocation, dry matter content and VWO tolerance. The most relevant difference between tolerant and susceptible cultivars was related to root system architecture.