Different species of the genus Monilinia are common plant pathogens that endanger pome and stone fruit production worldwide. In Serbia, two species of this genus are widely distributed - M. laxa and M. fructigena, while M. fructicola, which is officially on the A2 EPPO List of quarantine pest organisms in Europe and on the 1A part I List of quarantine pest organisms in Serbia, has so far been detected only on stored apple and nectarine fruits. The most important control measures against these pathogens include chemical control in combination with adequate cultural practices, particularly under favourable conditions for disease development. Concerning that species of this genus can cause significant economic losses, knowledge of the pathogen biology, disease epidemiology and pathogen-host interactions is a necessary prerequisite for stable and profitable production of pome and stone fruits.

Brown rot is one of the most important pre- and postharvest fungal diseases of stone fruit worldwide. In Serbia, where production of stone fruit is economically important, Monilinia laxa and M. fructigena are widely distributed. In surveys from 2011 to 2013, 288 isolates of Monilinia spp. were collected from 131 localities in 16 districts and from six hosts in Serbia. Using multiplex polymerase chain reaction, phylogenetic analysis, and morphological characterization, three species of Monilinia were identified as the causal agents of brown rot of stone fruit: M. laxa (89% of isolates), M. fructigena (3%), and M. fructicola (8%). In 2011, M. fructicola was reported for the first time on stone fruit in Serbia, with only one isolate detected. More isolates of M. fructicola were detected in 2012 (2 isolates) and 2013 (20 isolates). The presence of M. fructicola, as well as its increased frequency of detection during the survey, may indicate a change in the population structure of these pathogens, which could have an important impact on brown rot disease management in Serbia.

Considerable damping-off of the seedlings of several commercial Apiaceae plant species was observed in Serbia. The infection of a total of 48 seed samples of nine vegetable and spice plants with phytopathogenic Alternaria spp. was established using the deep-freeze-blotter method. Identification of Alternaria species was performed using both conventional methods and PCR. Four different plant-pathogenic Alternaria species were detected in Serbia: A. dauci, A. radicina, A. petroselini, and A. alternata, all of which caused reduction of carrot, parsley, parsnip, and celery seed emergence. Alternaria dauci, A. radicina, and A. petroselini were relatively more aggressive compared to A. alternata. Substantial seed infection levels and strong influence of Alternaria spp. on seed emergence indicated that production of Apiaceae seed needs to be improved in order to obtain pathogen-free seed.

In a survey to determine the presence and distribution of Iris yellow spot virus (IYSV) in greenhouse ornamentals and onion field crops in 14 districts of Serbia as well as on imported ornamental plants, 1,574 samples were collected and analyzed by double-antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA). IYSV was not detected in nearly 1,200 plant samples collected from 39 genera of ornamentals grown in greenhouses in Serbia or imported from other countries during 2005 to 2007. The virus was detected in samples from an onion seed crop in the Sirig locality (South Bačka District) that showed symptoms resembling those caused by IYSV and in samples without IYSV-like symptoms from an onion bulb crop in the Obrenovac locality (City of Belgrade District). Mechanical transmission of IYSV isolates was difficult, and only the isolate 605-SRB could infect four plant species, but not in all replications. No virus transmission could be demonstrated in 5,000 tested seeds originating from IYSV-infected onion crops. For further confirmation of IYSV, the nucleotide sequence of its nucleocapsid (NC) gene was obtained by reverse transcription–polymerase chain reaction (RT-PCR) in symptomatic onion samples as well as in symptomless leaves of Nicotiana benthamiana. Four previously developed primers were tested to determine their suitability for routine detection of Serbian IYSV isolates. Phylogenetic analysis showed clustering of isolates 605-SRB and 622-SRB from the onion seed crop and isolate 283-SRB from the onion bulb crop into two distant clades. The analysis indicated that Serbian isolates of IYSV do not share a recent common ancestor and that they represent two distinct lineages of IYSV in Serbia. Considering that onion is one of the most important and traditionally grown vegetable crops in Serbia, IYSV represents a potentially devastating pathogen in this country.

Tomato production worldwide is affected by numerous plant virus species. The early and accurate detection of viruses is a critical step for disease control. However, the simultaneous detection of the most known tomato viruses can be difficult because of the high number and diversity of tomato-infecting viruses. Here, we have identified four new viruses in Serbia by applying target-independent small RNA high-throughput sequencing (HTS). HTS was applied on pools of samples and separate samples, in total comprising 30 tomato samples that exhibited (severe) virus-like symptoms and were collected in Serbia during three annual surveys (2011 to 2013). These samples had previously tested negative for the presence of 16 tomato viruses using targeted detection methods. Three divergent complete genome sequences of Physostegia chlorotic mottled virus were obtained from different localities, indicating for the first time that this virus is widespread in Serbia and might represent an emergent viral pathogen of tomato. The tomato torrado virus was detected at one locality with devastating yield losses. The southern tomato virus was detected at two localities, and the spinach latent virus was detected at one locality. In addition, we detected the presence of one already-known virus in Serbia, the tomato spotted wilt orthotospovirus. All the HTS results were subsequently confirmed by targeted detection methods. In this study, the successful application of post hoc HTS testing of a limited number of pooled samples resulted in the discovery of new viruses. Thus, our results encourage the use of HTS in research and diagnostic laboratories, including laboratories that have limited resources to resolve disease etiology.[ ] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .