Tomato (Solanum lycopersicum) is one of the most economically important vegetables throughout the world. It is one of the best studied cultivated dicotyledonous plants, often used as a model system for plant research into classical genetics, cytogenetics, molecular genetics, and molecular biology. Tomato plants are affected by different pathogens such as viruses, viroids, fungi, oomycetes, bacteria, and nematodes, that reduce yield and affect product quality. The study of tomato as a plant-pathogen system helps to accelerate the discovery and understanding of the molecular mechanisms underlying disease resistance and offers the opportunity of improving the yield and quality of their edible products. The use of functional genomics has contributed to this purpose through both traditional and recently developed techniques, that allow the identification of plant key functional genes in susceptible and resistant responses, and the understanding of the molecular basis of compatible interactions during pathogen attack. Next-generation sequencing technologies (NGS), which produce massive quantities of sequencing data, have greatly accelerated research in biological sciences and offer great opportunities to better understand the molecular networks of plant–pathogen interactions. In this review, we summarize important research that used high-throughput RNA-seq technology to obtain transcriptome changes in tomato plants in response to a wide range of pathogens such as viruses, fungi, bacteria, oomycetes, and nematodes. These findings will facilitate genetic engineering efforts to incorporate new sources of resistance in tomato for protection against pathogens and are of major importance for sustainable plant-disease management, namely the ones relying on the plant’s innate immune mechanisms in view of plant breeding.

Plant viruses cause devastating diseases in many agriculture systems, being a serious threat for the provision of adequate nourishment to a continuous growing population. At the present, there are no chemical products that directly target the viruses, and their control rely mainly on preventive sanitary measures to reduce viral infections that, although important, have proved to be far from enough. The current most effective and sustainable solution is the use of virus-resistant varieties, but which require too much work and time to obtain. In the recent years, the versatile gene editing technology known as CRISPR/Cas has simplified the engineering of crops and has successfully been used for the development of viral resistant plants. CRISPR stands for ‘clustered regularly interspaced short palindromic repeats’ and CRISPR-associated (Cas) proteins, and is based on a natural adaptive immune system that most archaeal and some bacterial species present to defend themselves against invading bacteriophages. Plant viral resistance using CRISPR/Cas technology can been achieved either through manipulation of plant genome (plant-mediated resistance), by mutating host factors required for viral infection; or through manipulation of virus genome (virus-mediated resistance), for which CRISPR/Cas systems must specifically target and cleave viral DNA or RNA. Viruses present an efficient machinery and comprehensive genome structure and, in a different, beneficial perspective, they have been used as biotechnological tools in several areas such as medicine, materials industry, and agriculture with several purposes. Due to all this potential, it is not surprising that viruses have also been used as vectors for CRISPR technology; namely, to deliver CRISPR components into plants, a crucial step for the success of CRISPR technology. Here we discuss the basic principles of CRISPR/Cas technology, with a special focus on the advances of CRISPR/Cas to engineer plant resistance against DNA and RNA viruses. We also describe several strategies for the delivery of these systems into plant cells, focusing on the advantages and disadvantages of the use of plant viruses as vectors. We conclude by discussing some of the constrains faced by the application of CRISPR/Cas technology in agriculture and future prospects.

Tomato, one of the most cultivated and economically important vegetable crops throughout the world, is affected by a panoply of different pathogens that reduce yield and affect product quality. The study of tomato–pathogen system arises as an ideal system for better understanding the molecular mechanisms underlying disease resistance, offering an opportunity of improving yield and quality of the products. Among several genes already identified in tomato response to pathogens, we highlight those encoding the transcription factors (TFs). TFs act as transcriptional activators or repressors of gene expression and are involved in large-scale biological phenomena. They are key regulators of central components of plant innate immune system and basal defense in diverse biological processes, including defense responses to pathogens. Here, we present an overview of recent studies of tomato TFs regarding defense responses to biotic stresses. Hence, we focus on different families of TFs, selected for their abundance, importance, and availability of functionally well-characterized members in response to pathogen attack. Tomato TFs’ roles and possibilities related to their use for engineering pathogen resistance in tomato are presented. With this review, we intend to provide new insights into the regulation of tomato defense mechanisms against invading pathogens in view of plant breeding.

Grapevine trunk diseases (GTDs) are the most widespread fungal diseases, affecting grapevines in all the major growing regions of the world, and their complete eradication is still not possible. Aiming to search alternatives to avoid the spread and high incidence of these diseases, the present work intended to molecularly identify the grapevine endophytic community, the phytopathogenic fungi associated with GTDs in vineyards within the Alentejo region, and to test potential antagonist microorganisms as biological control candidates against GTDs-associated fungi. Grapevine endophytic community showed a wide variety of fungi in GTDs’ asymptomatic and symptomatic plants, nine of them previously described as GTDs-associated fungi. GTDs prevalent fungi identified in symptomatic plants were Diaporthe sp., Neofusicoccum sp., and H. viticola. Almost all these fungi were also detected in asymptomatic plants, which shows the importance of investigating the interactions of fungal communities and confirms the need for early diagnosis of these diseases. Direct inhibition antagonism tests were performed among identified endophytes and GTDs phytopathogenic fungi, and all the endophyte fungi showed potential as biocontrol agents. Our findings suggest that endophytes are promising candidates for their use in biological control due to their antagonistic activity against the mycelia growth of some GTDs-associated fungi.

Grapevine trunk diseases (GTDs) are among the most important problems that affect the longevity and productivity of vineyards in all the major growing regions of the world. They are slow-progression diseases caused by several wood-inhabiting fungi with similar life cycles and epidemiology. The simultaneous presence of multiple trunk pathogens in a single plant together with the inconsistent GTDs symptoms expression, their isolation in asymptomatic plants, and the absence of effective treatments make these diseases extremely complex to identify and eradicate. Aiming to gain a better knowledge of GTDs and search sustainable alternatives to limit their development, the present work studied the fungal community structure associated with GTDs symptomatic and asymptomatic grapevines, following a metagenomic approach. Two important cultivars from the Alentejo region with different levels of susceptibility to GTDs were selected, namely, ‘Alicante Bouschet’ and ‘Trincadeira’. Deep sequencing of fungal-directed ITS1 amplicon led to the detection of 258 taxa, including 10 fungi previously described as responsible for GTDs. Symptomatic plants exhibited a lower abundance of GTDs-associated fungi, although with significantly higher diversity of those pathogens. Our results demonstrated that trunk diseases symptoms are intensified by a set of multiple GTDs-associated fungi on the same plant. The composition of fungal endophytic communities was significantly different according to the symptomatology and it was not affected by the cultivar. This study opens new perspectives in the study of GTDs-associated fungi and their relation to the symptomatology in grapevines.

The sustainability of agriculture requires the adoption of agricultural soil conservation practices with positive impacts on soil quality, which can promote beneficial soil microbiota like arbuscular mycorrhizal fungi (AMF) and its diversity. This study aims to assess the influence of the presence of intact extraradical mycelium as a preferential source of inoculum of the native AMF in order to guarantee a better colonization as well as its possible bioprotective effect against Magnaporthiopsis maydis. In order to vary the available extraradical mycelium, two experiments, with and without cover crop, were carried out, in which two tillage systems and two maize varieties were studied. The capitalization of the benefits, in terms of grain production and M. maydis presence, associated to the cover crop were only achieved with minimum tillage. Therefore, both cultural practices are necessary to reduce the fungus presence, coupling the effect of mycorrhization together with other benefits associated with the cover crop. Although in the absence of a cover crop and using conventional tillage, yields and lower levels of M. maydis are possibly achieved, this system is more dependent on the variety used, does not benefit from the advantages associated with the cover crop, is more expensive, and environmentally unsustainable.