Pepper (Capsicum spp.) is one of the major vegetable crops grown worldwide largely appreciated for its economic importance and nutritional value. This crop belongs to the large Solanaceae family, which, among more than 90 genera and 2500 species of flowering plants, includes commercially important vegetables such as tomato and eggplant. The genus includes over 30 species, five of which (C. annuum, C. frutescens, C. chinense, C. baccatum, and C. pubescens) are domesticated and mainly grown for consumption as food and for non-food purposes (e.g., cosmetics). The main challenges for vegetable crop improvement are linked to the sustainable development of agriculture, food security, the growing consumers’ demand for food. Furthermore, demographic trends and changes to climate require more efficient use of plant genetic resources in breeding programs. Increases in pepper consumption have been observed in the past 20 years, and for maintaining this trend, the development of new resistant and high yielding varieties is demanded. The range of pathogens afflicting peppers is very broad and includes fungi, viruses, bacteria, and insects. In this context, the large number of accessions of domesticated and wild species stored in the world seed banks represents a valuable resource for breeding in order to transfer traits related to resistance mechanisms to various biotic stresses. In the present review, we report comprehensive information on sources of resistance to a broad range of pathogens in pepper, revisiting the classical genetic studies and showing the contribution of genomics for the understanding of the molecular basis of resistance.

Application of organic amendments is considered an eco-friendly practice to promote soil fertility and suppressiveness against a wide range of soil-borne pathogens. However, limited information is available about the capabilities of organic amendments to control virus disease. In this study, the suppressiveness of different organic amendments (i.e., compost manure, biochar, alfalfa straw, and glucose) was determined against the Tomato spotted wilt virus (TSWV) on tomato plants in a 1-year-long mesocosm experiment. Organic treatments were compared to the ordinary soil management based on mineral fertilizers and fumigation. Tomato seedlings were inoculated with TSWV and the infection and symptoms were assessed three weeks later. The disease incidence was higher in soil treated with mineral fertilizers and fumigation (>80%) compared to the application of organic amendments, with alfalfa straw and biochar recording the lowest incidence (<40%). Moreover, soil microbiota structure and diversity were assessed by high-throughput sequencing of bacterial and eukaryotic rRNA gene markers. Several members belonging to the bacterial phyla of Acidobacteria, Actinobacteria, Bacteroidetes, and Proteobacteria, as well as members of the fungal genus Acremonium, were positively associated with plant health. This study showed that conventional practices, by shifting microbiome composition, may increase TSWV incidence and severity.

Citrus concave gum-associated virus (CCGaV) is a negative-stranded RNA virus, first reported a few years ago in citrus trees from Italy. It has been reported in apple trees in the USA and in Brazil, suggesting a wider host range and geographic distribution. Here, an anti-CCGaV polyclonal antiserum to specifically detect the virus has been developed and used in a standard double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) that has been validated as a sensitive and reliable method to detect this virus both in citrus and apple trees. In contrast, when the same antiserum was used in direct tissue-blot immunoassay, CCGaV was efficiently detected in citrus but not in apple. Using this antiserum, the first apple trees infected by CCGaV were identified in Italy and the presence of CCGaV in several apple cultivars in southern Italy was confirmed by field surveys. High-throughput sequencing (HTS) allowed for the assembling of the complete genome of one CCGaV Italian apple isolate (CE-c3). Phylogenetic analysis of Italian CCGaV isolates from apple and citrus and those available in the database showed close relationships between the isolates from the same genus (Citrus or Malus), regardless their geographical origin. This finding was further confirmed by the identification of amino acid signatures specific of isolates infecting citrus or apple hosts. Analysis of HTS reads also revealed that the CE-c3 Italian apple tree, besides CCGaV, was simultaneously infected by several viruses and one viroid, including apple rubbery wood virus 2 which is reported for the first time in Italy. The complete or almost complete genomic sequences of the coinfecting agents were determined.