Hop (Humulus lupulus) is an important economic crop in Slovenia, especially in brewing. Diseases caused by fungi, viruses, and viroids represent a serious obstacle for growing hops, which is why their rapid and reliable detection is important. The purpose of this thesis is to review and compare modern and molecular methods under development for the detection of the most important hop pathogens (Verticillium spp., Fusarium spp., HLVd, CBCVd, HSVd, HpMV). Conventional visual and serological methods are generally insufficient in terms of sensitivity, especially in the early stages of infection and latent infections. The gold standard for pathogen detection in hops is currently represented by PCR methods and their upgrades (qPCR, RT-qPCR), which are most commonly used in routine diagnostics and enable specific and quantitative detection of pathogens, even at low concentrations of target nucleic acid. A comparison of methods has shown that newer diagnostic approaches, such as isothermal amplification-based methods, CRISPR-Cas detection systems and nanomaterial genosensors, offer rapid and specific detection possibilities in the field. Bioinformatics tools based on high-throughput sequencing are an important tool in research diagnostics and the identification of new pathogens. These approaches have great potential for use in the diagnosis of pathogens in hops, but require further validation and standardization before their routine application.
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