Raspberry bushy dwarf virus (RBDV) is an economically significant pathogen of raspberry and grapevine, and it has also been found in cherry. Most of the currently available RBDV sequences are from European raspberry isolates. This study aimed to sequence genomic RNA2 of both cultivated and wild raspberry in Kazakhstan and compare them to investigate their genetic diversity and phylogenetic relationships, as well as to predict their protein structure. Phylogenetic and population diversity analyses were performed on all available RBDV RNA2, MP and CP sequences. Nine of the isolates investigated in this study formed a new, well-supported clade, while the wild isolates clustered with the European isolates. Predicted protein structure analysis revealed two regions that differed between α- and β-structures among the isolates. For the first time, the genetic composition of Kazakhstani raspberry viruses has been characterized.

Wild apples and their hybrids are valued as a source of genetic resistance to biotic and abiotic stress. Malus niedzwetzkyana is an endangered ornamental apple species endemic to Southeast Kazakhstan, the center of Malus domestication. To test the fire blight resistance of M. niedzwetzkyana, eight plant genotypes were inoculated with a local strain of Erwinia amylovora. The genotypes possess different genetic backgrounds, which was confirmed via SSR profiling. Four out of eight displayed moderate to severe symptoms of fire blight infection, while the three wild genotypes proved resistant. To search for the source of the resistance, the samples were tested for the presence of FBF7 QTL using SCAR markers, where seven genotypes tested positive for one of the markers (AE10-375) and one for the other (GE80-19). No correlation between resistance phenotype and FBF7 QTL was confirmed, indicating the source lies elsewhere. Developing detailed genetic and phenotypic profiles of wild apple species helps advance both the preservation efforts and marker-assisted selection in apple breeding.

Wheat is an essential cereal crop for the economy and food safety of Kazakhstan. In the present work, a screening of wheat and barley from different regions of Kazakhstan was conducted using newly developed specific primers for reverse transcription PCR and loop-mediated isothermal amplification (LAMP) assays. In total, 82 and 19 of 256 samples of wheat and barley tested positive for wheat streak mosaic virus (WSMV) and barley stripe mosaic virus (BSMV), respectively. A phylogenetic analysis using two independent methods revealed that most of the analyzed isolates had a European origin. Molecular data on the distribution and diversity of cereal viruses in Kazakhstan were obtained for the first time and will help lay a foundation for the implementation of genetics and genomics in wheat phyto-epidemiology in the country.

Kazakhstan is recognized as one of the primary centers of origin of the wild apple Malus sieversii, concentrated mainly in the mountains like Trans-Ile and Zhongar Alatau, as well as parts of the Tarbagatay, Talas Alatau, and Karatau ranges. As the wild progenitor of Malus domestica, M. sieversii harbors a critical genetic diversity essential for apple breeding and conservation efforts. However, its natural populations are increasingly threatened by latent viral infection, which weakens trees, reduces reproduction, and hinders regeneration. In this study, the spread of apple chlorotic leaf spot virus (ACLSV) and apple stem pitting virus (ASPV) was documented in four wild apple populations, with detection rates of 50.2% and 42.2%, respectively. Mixed infections were observed in 28.8% of sampled trees. Apple stem grooving virus (ASGV) was detected exclusively in cultivated orchards, whereas apple mosaic virus (ApMV) and apple necrotic mosaic virus (ApNMV) were not found in either wild forests or cultivated orchards. Using Geographic Information System (GIS) technology, we developed the first spatial distribution maps of these viruses in wild apple forests in the Tian Shan region, revealing site-specific variation and infection rates. These results underscore the importance of monitoring viral infections in wild M. sieversii populations to preserve genetically valuable, virus-free germplasm critical for apple breeding, crop improvement, and sustainable orchard management.

Apples (Malus spp.) are one of the popular fruits in the world. Apple cultivars face significant threats from various viruses and virus-like diseases. These include well-known ones such as Apple mosaic virus (ApMV), Apple necrotic mosaic virus (ApNMV), Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV), and Apple chlorotic leaf spot virus (ACLSV). These viruses are known to infect a wide range of apple cultivars, leading to various symptoms such as stem grooving, chlorotic leaf spots, stem pitting, and mosaic patterns on the fruits and leaves. The objective of this study was to assess the incidence of the five viruses in apple-growing regions of southern Kazakhstan. The average positive rates of ACLSV, ASPV and ASGV were 42.1%, 57% and 12.6% respectively. ApMV and ApNMV were not detected. The study revealed a high incidence of mixed infections of the three apple viruses in Kazakhstan, with 60.6% of the infected apple plants harboring more than one species of virus. The most frequent virus combination was ACLSV+ASPV, with an incidence of 31.7%, followed by ACLSV+ASGV (10.9%), ASPV+ASGV (10%) and ACLSV+ASPV+ASGV (8.2%). The high prevalence of single and mixed infections in surveyed regions underscores the need for comprehensive and integrated approaches to disease management such as multiplex RT-PCR. The assay allows for the simultaneous detection of multiple apple viruses in a single reaction, providing a rapid and efficient means of screening for multiple pathogens in apple plants.

This study presents an integrative investigation of four rare and threatened plant species—Taraxacum kok-saghyz L.E. Rodin, Astragalus rubtzovii Boriss., Schmalhausenia nidulans (Regel) Petr., and Rheum wittrockii Lundstr.—native to the Ile Alatau and Ketmen ridges of the Northern Tian Shan in Kazakhstan. Combining chloroplast genome sequencing, geobotanical surveys, and anatomical and population structure analyses, we aimed to assess the ecological adaptation, genetic distinctiveness, and conservation status of these species. Field surveys revealed that population structures varied across species, with T. kok-saghyz and S. nidulans dominated by mature vegetative and generative individuals, while A. rubtzovii and R. wittrockii exhibited stable age spectra marked by reproductive maturity and ongoing recruitment. Chloroplast genome assemblies revealed characteristic patterns of plastid evolution, including structural conservation in S. nidulans and R. wittrockii, and a reduced inverted repeat region in A. rubtzovii, consistent with its placement in the IR-lacking clade of Fabaceae. Morphological and anatomical traits reflected habitat-specific adaptations such as tomentose surfaces, thickened epidermis, and efficient vascular systems. Despite these adaptations, anthropogenic pressures including overgrazing and habitat degradation pose significant risks to population viability. Our findings underscore the need for targeted conservation measures, continuous monitoring, and habitat management to ensure the long-term survival of these ecologically and genetically valuable endemic species.