Grafting cultivars onto rootstocks is a widely used practice by the apple industry predominantly aimed at faster fruit bearing. Using high-throughput sequencing, we revealed the presence of recently described viral agents, namely apple hammerhead viroid (AHVd), apple luteovirus 1 (ALV-1), and citrus concave gum-associated virus (CCGaV), in germplasm collections and production orchards in the Czech Republic and Hungary. The HTS results were validated with RT-(q)PCR, and Northern blotting techniques. To obtain further insight about the presence of these agents, RT-PCR based surveys were carried out and showed their widespread presence alone or in mixed infections. The pathogens were present both in production areas and in feral samples. In addition, rootstock-to-scion transmission of ALV-1 and CCGaV was confirmed using commercial rootstock materials. Phylogenetic relationships based on partial sequences of distinct variants were also investigated. Furthermore, the rosy apple aphid was found to be ALV-1-positive, suggesting that it might be a potential vector of the virus.

Czech Academy of Sciences Biology Centre Institute of Plant Molecular Biology Branišovská 31 37005 České Budějovice Czech Republic

Genomics Research Group Department of Plant Pathology Institute of Plant Protection Hungarian University of Agriculture and Life Sciences Szent Gyorgyi Albert Street 4 2100 Gödöllő Hungary

Research and Breeding Institute of Pomology Holovousy Ltd Holovousy 129 50801 Holovousy Czech Republic

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