Apple (Malus domestica Borkh.) production is increasingly threatened by fungal diseases under conditions of intensive horticulture and ongoing climate change. In southeastern Kazakhstan, symptoms associated with Alternaria spp. have become more frequent in commercial orchards; however, molecularly confirmed data on the pathogen associated with these symptoms remain limited. This study aimed to identify, using multigene molecular phylogenetic analysis, an Alternaria isolate obtained from infected apple leaves and fruits, to confirm its pathogenicity experimentally, and to compare the susceptibility of apple cultivars to this pathogen. For molecular identification, nucleotide sequences of four genetic markers—the ITS region of rDNA, SSU, tef1-α, and RPB2—were obtained by PCR and sequencing. The sequences were compared with reference data from the GenBank database using BLASTn, and phylogenetic relationships were inferred using the maximum likelihood method based on a concatenated dataset of the four loci. The isolate KZ17 clustered within the A. alternata clade, with the broader node uniting this group with A. gossypina and A. longipes receiving a bootstrap value of 78%. A total of 20 fungal isolates were obtained from 112 symptomatic apple leaf and fruit samples. Among them, one representative isolate, KZ17, was selected for multilocus molecular identification and pathogenicity testing. The pathogenicity of isolate KZ17 was confirmed in inoculation experiments on apple microshoots under controlled conditions. Artificial inoculation of detached leaves and ripe fruits of 14 apple cultivars revealed significant cultivar-dependent differences in susceptibility. Lesion diameters ranged from 12.3 ± 0.20 to 19.2 ± 0.35 mm on detached leaves and from 15.0 ± 1.2 to 30.0 ± 2.4 mm on ripe fruits. The least susceptible cultivars were ‘Granny Smith’, ‘Zaman’, and ‘Maksat’, whereas ‘Voskhod’, ‘Saltanat’, and ‘Kamila’ showed the greatest susceptibility. These differences were statistically significant (p < 0.001). This study provides the first multigene-based confirmation of the association of A. alternata with apple leaf and fruit lesions in southeastern Kazakhstan and demonstrates cultivar-dependent differences in susceptibility to this pathogen. These findings contribute to improved pathogen diagnostics, germplasm screening for resistance, and the development of plant protection strategies for commercial apple orchards.

Эффективная защита плодов от поражения при хранении достигается путем проведения защитных мероприятий в течении вегетации, особенное значение имеют обработки в послеуборочный период. В статье представлены результаты оценки эффективности биологического препарата «Биоконсерванта МР-3» на основе дрожжей (Metschnikowia pulcherrima) для контроля комплекса гнилей плодов яблони, развивающихся при хранении. Объектами исследований являются болезни инфекционного и не инфекционного происхождения, влияющие на длительность сроков хранения плодов. Были взяты три сорта: «Апорт», «Восход», «Талгарское» для проведения наблюдения за лежкостью плодов и степенью их поражения различными болезнями при хранении. Хранение осуществлялось при температуре +1-2°С и относительной влажности 90-95%. Проводились работы по уточнению видового состава болезней, определению естественной убыли массы плодов, изменения твердости мякоти, были проведены биохимические анализы. Твердость мякоти плода измеряли измерителем (penetrometer). Перед закладкой на хранение плоды были обработаны биологическим препаратом Биоконсервант МР-3 в двух формах жидкой и сухой, обработка проводилась путем замачивания плодов в биологическом препарате на 30 секунд, норма расхода препарата Биоконсервант МР-3 (сухой формы -100 г/10 л/воды) и (жидкой формы 100 мл/10 л/воды) кроме контрольного варианта, плоды были заложены в холодильник для проведения дальнейшего наблюдения.

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.

The development of intensive horticulture in Kazakhstan requires the use of virus-free planting material, particularly apple rootstocks (Malus domestica), free of viral and viroid infections. Latent forms of pathogens, which do not exhibit visible symptoms but are easily transmitted through vegetative propagation, are consid ered the most hazardous. The objective of this study was to evaluate the phytosanitary status of apple root stocks used in nurseries in southern Kazakhstan by employing reverse transcription quantitative polymerase chain reaction (RT-qPCR). A total of 24 samples from field and laboratory collections were analyzed. RNA extraction was performed using the “PhytoSorb®” kit, and diagnostics were conducted on the Bio-Rad CFX96 platform using multiplex LETGEN test kits. Four pathogens were identified: Apple chlorotic leaf spot virus (ACLSV), Apple stem pitting virus (ASPV), Apple green crinkle associated virus (AGCaV), and Apple hammerhead viroid (AHVd). The viruses ASPV and AGCaV were found to be the most prevalent, occurring in both field and laboratory samples. These findings confirm the widespread circulation of these pathogens within the apple rootstock propagation system. The results emphasize the need for the implementation of regular molecular diagnostics, sanitation programs, and certification measures aimed at preventing the spread of latent infections and ensuring the sustainable development of horticulture in the region.

In commercial orchards and nurseries, the spread of viral infections in apple (Malus domestica Borkh.) poses a serious threat to plant phytosanitary status and productivity. The aim of this study was to obtain virus-free apple rootstock planting material and to evaluate the effectiveness of integrated in vitro biotechnological methods of plant sanitation. The objects of the study were apple rootstocks from pomological and in vitro collections in Kazakhstan. The highest viral load was detected in rootstock B-16-20. For sanitation, a combined Thermotherapy + Chemotherapy + SAM method with antiviral agents was applied. The results showed that the effectiveness and phytotoxicity of the methods depend on the combination of techniques and the concentration of the applied agents. The obtained data confirm the high efficiency of integrated biotechnological approaches for obtaining virus-free apple planting material and have practical significance for certified propagation of fruit crops in Kazakhstan.