Determination of the Distribution of Viral Infections in the Apple Rootstock Nursery System in Kazakhstan Using RT-qPCR

The phytosanitary quality of apple rootstocks is a key determinant of sustainable orchard production, as latent viral and viroid infections are readily transmitted through vegetative propagation. In Kazakhstan, systematic molecular monitoring of apple rootstock material remains limited. The aim of this study was to assess the prevalence of major viral and viroid pathogens in apple rootstocks used in nursery systems in Kazakhstan using RT-qPCR. Molecular testing covered nine regulated viruses and viroids of the genus Malus. Positive results were obtained for four pathogens: Apple chlorotic leaf spot virus (ACLSV), Apple stem pitting virus (ASPV), Apple green crinkle-associated virus (AGCaV) and Apple hammerhead viroid (AHVd). AGCaV was the most widespread, being detected in the majority of the samples, whereas AHVd was observed only sporadically, with a borderline amplification signal indicating a very low viroid titre, and is reported here for the first time in Kazakhstan. The detection of ASPV and ACLSV confirms the presence of mixed latent infections in apple rootstock material. These findings highlight the presence of hidden viral infections in nursery material and underscore the urgent need for a national certification system, regular molecular monitoring and the development of in vitro sanitation programmes. Such measures are essential to ensure the phytosanitary safety and competitiveness of Kazakhstan's fruit production sector.