Fire blight disease of apples continues its worldwide spread, having reached Kazakhstan in 2010. It is a great threat to the wild apple forests of Malus sieversii. The introduction of fire blight is already showing a considerable impact on cultural apple growing and demands radical efforts for conservation of the wild apple forests. A number of studies have been conducted to examine the presence of fire blight distribution within apples in agricultural areas; however, there has been no large-scale monitoring of wild apple tree populations. Here we present the results of three years of monitoring wild apples in three protected areas of Kazakhstan, looking for the presence of fire blight (Erwinia amylovora). A visual inspection showed no signs of fire blight on the trees of M. sieversii in three consecutive years. These findings were confirmed by lateral flow immunochromatography, and conventional and real-time polymerase chain reaction tests of the asymptomatic samples. The findings of this study will be used to produce recommendations for state authorities to prevent fire blight in wild apple forests of Kazakhstan.

Rootstocks play an important role in the life of fruit crops.The full realization of the potential of the variety depends on them, such as physiological capabilities, drought resistance, winter hardiness, productivity, durability and fruiting rate. To determine the best scion-rootstock combinations physiological and phyto-pathological assessment scion-rootstock combinations for apple cv. ‘Aport’ and M. sieversii were studied. The experiment was carried out from February 2019 to July 2022 in the experimental orchard of Kazakh Fruit and Vegetable Research Institute. In the experimental garden (2015 y. planted) the physiological studies of the water homeostasis, adaptive potential, ecological status, and coefficient stress were carried out in dynamics. High adaptive homeostatic coefficients and a good ecological state were observed in forms № 1, 8, 11 and № 9 throughout the growing season. The robustness of these forms was on an average 38% higher than that of the № 2, 3, 4 and № 7. The maximum fetal weight was 270 g. According to biochemical analysis, forms № 2, 11 and № 9 differed in the amount of vitamin C and total sugar. Scab and powdery mildew are common ‘Aport’ diseases. Forms № 11, 2, 10 are the most resistant rootstock-scion combinations. To conclude, № 8, 9 and № 11 were considered as highly adaptive, productive, rapid-fruiting and resistant to biotic and abiotic factors, free-subsurface factors. These varieties were collected from the Reserves of State National Parks of Kazakhstan.

Viral infections in stone fruit crops cause substantial economic losses across all sectors of production. Despite their significance, viruses affecting stone fruits remain under-investigated in Kazakhstan. Among these, plum pox virus (PPV, genus Potyvirus, family Potyviridae), commonly known as Sharka, is the most critical viral pathogen worldwide, severely threatening the sustainable cultivation of stone fruits and posing risks to food security. This study aimed to evaluate virus management strategies in stone fruit crops to facilitate the production of healthy planting material from valuable genotypes. Field surveys were conducted in plum and apricot orchards located in the Almaty region (Southeast Kazakhstan) and the Saryagash region (Southern Kazakhstan). Plant samples were tested for the presence of the following viruses: apple chlorotic leaf spot virus (ACLSV), apple mosaic virus (ApMV), PPV, prune dwarf virus (PDV), prunus necrotic ringspot virus (PNRSV), cherry green ring mottle virus (CGRMV), and myrobalan latent ringspot virus (MLRSV). Real-time RT-PCR diagnostics confirmed the presence of PPV in the ‘Stanley’ and ‘Ansar’ cultivars and Prunus armeniaca genotypes, while both PPV and ACLSV were detected in the ‘Ayana’ variety. Chemotherapy (Ribavirin), thermotherapy, cryotherapy, and shoot apical meristem (SAM) culture, both individually and in combination, were used to eliminate viruses and regenerate virus-free plants. Successful virus eradication was achieved for PPV and ACLSV. However, the ‘Stanley’ and ‘Ansar’ cultivars did not survive the treatment process, likely due to high thermo- or cryo-sensitivity. As a result of this research, an in vitro collection of virus-free plants was established, comprising eight rootstocks, six plum cultivars, and three apricot genotypes.

In the present study, the most valuable cultivar ‘Aport krovavo-krasnyy’ was grafted onto M. sieversii genotypes harvested from 11 populations in Dzungarian Alatau and Ile Alatau to identify ones resistant to Erwinia amylovora. The wild apple populations included in the present research have not been previously explored. Seedling population 10, developed using rootstocks from a M. sieversii population growing in Turgen, demonstrated the highest resistance to Erwinia amylovora, showing no fire blight symptoms and no positive PCR results for E. amylovora during the eight years of monitoring in the Talgar field (Kazakhstan) from 2015 to 2022. The population from Steep Tract (seedling population 1) was also valuable for breeding and reduced the pathogen distribution to below 30%. Genotypes from a genetic reserve (seedling population 5) were the most susceptible among the researched populations, with a disease distribution level of 24–95%. In seedling population 5, trees affected at least twice by the pathogen exhibited wilting, shepherd’s crook formation, leaf necrosis, and occasional exudate droplets, while trees in other combinations primarily showed shoot wilting and leaf death. Fire blight disease also developed more rapidly within the plant in seedling population 5; by 2020, one tree nearly died after only two infections.

Apple (Malus domestica Borkh.) rootstocks play a key role in modern intensive orchard systems, where their accurate identification is essential for breeding, nursery production, and certification of planting material. This is particularly important in Kazakhstan, a recognized center of origin of cultivated apple, where local germplasm remains insufficiently characterized at the molecular level. In this study, we integrated simple sequence repeat (SSR) genotyping and morphological trait analysis to develop a reliable approach for the identification of clonal apple rootstocks cultivated in Kazakhstan. Five widely used rootstocks (Zhetysu 5, ARM-18, B-7-35, M9, and B9) were analyzed using 17 polymorphic SSR markers and 30 vegetative traits. SSR analysis revealed moderate genetic polymorphism (PIC = 0.28–0.54; He = 0.35–0.58) and enabled clear discrimination among all studied genotypes. Cluster analysis based on genetic distances grouped rootstocks according to their genetic similarity, reflecting their origin and differentiation. Morphological evaluation demonstrated significant phenotypic variability and identified correlations among key vegetative traits related to plant vigor and leaf development. The integration of molecular and morphological data allowed the development of comprehensive genotype profiles (“molecular–morphological passports”) for each rootstock, ensuring their reliable identification. The proposed approach provides a practical framework for the certification of planting material and the management of apple genetic resources in Kazakhstan. It can be applied to improve nursery systems, support breeding programs, and ensure the production of true-to-type planting material in modern horticulture.

Latent viral and viroid infections represent a major phytosanitary threat to pome fruit production because infected propagation material facilitates the long-term spread of pathogens in orchards. This study investigated the prevalence of viral and viroid pathogens in apple and pear orchards of southern and southeastern Kazakhstan and evaluated the efficiency of integrated in vitro sanitation approaches. A total of 34 samples collected from commercial orchards were analyzed using RT-qPCR. Apple stem pitting virus (ASPV) was the most prevalent pathogen detected across all surveyed regions, followed by Apple chlorotic leaf spot virus (ACLSV). Apple stem grooving virus (ASGV), Apple hammerhead viroid (AHVd), Apple mosaic virus (ApMV), and Apple rubbery wood virus 1 (ARWV-1) were detected at lower frequencies. Notably, ARWV-1 and AHVd were detected exclusively in the Almaty Region, representing their first molecular detection in Kazakhstan. Mixed infections were common, and visual symptoms did not consistently correlate with molecular detection results, emphasizing the importance of RT-qPCR for reliable phytosanitary diagnostics. Integrated sanitation methods combining thermotherapy, chemotherapy, cryotherapy, and meristem culture effectively eliminated viral and viroid infections from infected apple and pear genotypes. Ribavirin at 15 mg L⁻¹ provided the optimal balance between antiviral activity and explant viability. Complete elimination of ACLSV, AHVd, ASPV, ASGV, ApMV, and ARWV-1 was achieved after combined treatment, while regenerated plants maintained stable micropropagation capacity. The obtained results demonstrate the necessity of routine molecular monitoring and support the development of virus-free certification systems for pome fruit crops in Kazakhstan.