Cannabis (Cannabis sativa L.) is a dicotyledonous angiosperm originating from Central Asia but is cultivated across many parts of the world due to its ability to grow in a wide range of habitats and environmental conditions [1].

Cannabis belongs to the Cannabaceae family and is considered one of the earliest cultivated crops, being of particular interest due to its multiple uses. Cannabinoids are responsible for the pharmacological and psychoactive properties of this crop, and these therapeutic characteristics have drawn the attention of researchers from all over the world. Additionally, hemp, a Cannabis variety containing less than 0.3% of tetrahydrocannabinol (THC), is cultivated for biomass and fibre, which constitute feedstock for industrial uses. Conversely, medicinal Cannabis contains a greater amount of THC, which has been increasing in recent years, reaching 17–28% of the dry weight in some varieties [2], or even exceeding 30% in others [3].

Among the ~130 secondary metabolites identified in Cannabis [4], THC, along with cannabidiol (CBD), constitute the most relevant compounds produced by this crop and are the main focus of Cannabis breeding programs.

Breeding efforts to produce Cannabis with unique fragrance and flavour characteristics are also of interest. Consequently, the profile of terpenoids, which are highly abundant and largely responsible for the characteristic aroma of Cannabis, is of importance, with isoprenes, monoterpenes, and sesquiterpenes being the predominant classes [5,6].

Due to the legislation regulating Cannabis and related breeding programs, research into the cannabinoid biosynthetic pathway is underrepresented, and it has not been sufficiently characterised, especially at the molecular level [5,7]. Many other major crops have already been widely investigated from this perspective, especially after the advent of Next Generation Sequencing (NGS) technologies [7]. However, the recent modifications in legislation and less stringent regulations [8], as well as the availability of the Cannabis genomic sequence [9], have broadened research in this crop, with the aim also to improve its biomass quality, in the context of sustainable agriculture [10,11].

These legislative changes have also resulted in increased Cannabis production and, with it, a growth of the incidence and severity of crop pathogens, along with the detection of previously unreported diseases. Among emerging pathogens of Cannabis recently reported there are Botrytis cinerea [12,13], Fusarium spp. [14,15], Pythium [16,17] Golovinomyces spp. [12,13], and Hop latent viroid [18], where hop (Humulus lupulus) is a member of Cannabaceae and is closely related to Cannabis [19]. These pathogens can be grouped according to the tissues they infect: root and crown (Fusarium oxysporum, Fusarium proliferatum, Fusarium solani, Pythium myriotylum, Pythium dissotocum, Pythium aphanidermatum), leaves (Golovinomyces spp.), buds (Hop latent viroid) [12]. Botrytis cinerea is often classified as a postharvest pathogen and can attack Cannabis seeds, leaves, and stalks [12]. Fusarium and Pythium species are the most destructive root pathogens, especially when the infection occurs during vegetative growth. Crop losses resulting from the attack of these two pathogens can reach 30% of the total yield [12]. Botryis and Fusarium species also are harmful, as well as other fungi, such as Golovinomyces species, causing powdery mildew (PM, a common term for several taxa of plant pathogenic fungi), and colonizing foliar and flower tissues through the production of spores. Furthermore, extensive infection by fungi such as Fusarium can lead to mycotoxin accumulation in the tissues, potentially harmful to human health [20]. Hop latent viroid leads to malformation of buds and can infect other parts of the crop [18].

The above-reported fungi, oomycetes and the mentioned viroid have been investigated in Cannabis, as well as in several other crops, but little is known about infection within the seed, even though there are harmful pathogens, such as Alternaria, which can start their attack in developing seedlings [12]. The lack of significant research results on Cannabis bacteria pathogen defence mechanisms has also been underlined [21].

On the other hand, research into the characterization and use of biocontrol agents has consistently improved in recent years [22]. The use of synthetic fungicides to control fungal diseases has limitations due to toxicological risks, and it is necessary to replace them with safer means, for human health and with reduced environmental risks. Omics methods and their applications in the biocontrol field were recently reviewed by Massart et al. [23]. A better understanding of the molecular mechanisms underlying pathogen plant resistance can only have positive effects in this field of research.

Many of the above-reported pathogens have been identified using methods based on Polymerase Chain Reaction (PCR) of parts of rDNA, such as Internal Transcribed Spacer (ITS) and Inter Generic Spacer (IGS) regions [24]. However, for Golovinomyces and Botrytis, additional molecular markers were necessary to differentiate between species [25,26].