The genus Alternaria is a widely distributed major plant pathogen that can act as a saprophyte in plant debris. Fungi of this genus frequently infect cereal crops and cause such diseases as black point and wheat leaf blight, which decrease the yield and quality of cereal products. A total of 25 Alternaria sp. isolates were collected from germ grains of various wheat cultivars from different geographic regions in Kazakhstan. We investigated the genetic relationships of the main Alternaria species related to black point disease of wheat in Kazakhstan, using the inter-primer binding site (iPBS) DNA profiling technique. We used 25 retrotransposon-based iPBS primers to identify the differences among and within Alternaria species populations, and analyzed the variation using clustering (UPGMA) and statistical approaches (AMOVA). Isolates of Alternaria species clustered into two main genetic groups, with species of A.alternata and A.tennuissima forming one cluster, and isolates of A. infectoria forming another. The genetic diversity found using retrotransposon profiles was strongly correlated with geographic data. Overall, the iPBS fingerprinting technique is highly informative and useful for the evaluation of genetic diversity and relationships of Alternaria species.

Analysis of the genetic diversity of natural populations of threatened and endangered species of plants is a main aspect of conservation strategy. The endangered species Allium altaicum is a relict plant of the Ice Age and natural populations are located in extreme climatic conditions of Kazakstan’s Altai Mountains. Mobile genetic elements and other interspersed repeats are basic components of a eukaryote genome, which can activate under stress conditions and indirectly promote the survival of an organism against environmental stresses. Detections of chromosomal changes related to recombination processes of mobile genetic elements are performed by various PCR methods. These methods are based on interspersed repeat sequences and are an effective tool for research of biological diversity of plants and their variability. In our research, we used conservative sequences of tRNA primer binding sites (PBS) when initializing the retrotransposon replication as PCR primers to research the genetic diversity of 12 natural populations of A. altaicum found in various ecogeographic conditions of the Kazakhstani Altai. High efficiency of the PBS amplification method used was observed already at the intrapopulation level. Unique amplicons representative of a certain population were found at the intrapopulation level. Analysis of molecular dispersion revealed that the biodiversity of populations of mountainous and lowland A. altaicum is due to intrapopulation differences for climatic zones of habitation. This is likely conditional upon predominance of vegetative reproduction over seed reproduction in some populations. In the case of vegetative reproduction, somatic recombination related to the activity of mobile genetic elements are preserved in subsequent generations. This leads to an increase of intrapopulation genetic diversity. Thus, high genetic diversity was observed in populations such as A. altaicum located in the territory of the Kalbinskii Altai, whereas the minimum diversity was observed in the populations of the Leninororsk ecogeographic group. Distinctions between these populations were also identified depending on the areas of their distribution. Low-land and mid-mountain living environments are characterized by a great variety of shapes and plasticity. This work allowed us to obtain new genetic data on the structure of A. altaicum populations on the territory of the Kazakhstan Altai for the subsequent development of preservation and reproduction strategies for this relict species.

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Species of the genus Alternaria are widely distributed as saprophytes on plant residues, as well as pathogens of various plant species. On wheat seeds, Alternaria fungi are localized in the endosperm and fruit shells, causing symptoms of "black germ" disease, and are a dominant component of the wheat seed microbiome. Recently, due to the high potential danger of these fungi, much attention has been paid to the study of the genetic variability of populations that exist in certain climatic conditions. Using retrotransposon sequences as markers increase knowledge about phylogenetic relationships within populations of phytopathogenic fungi, as well as their biodiversity. The iPBS (inter-priming binding sites) method used in this work was applied to detect genetic polymorphism of isolates of the genus Alternaria, as the most frequently encountered genus (the frequency of isolation was more than 50%). The isolates were isolated from wheat seeds that were cultivated in various ecological regions. The 4 iPBS primers used in this study amplified 387 fragments, 352 of which were polymorphic. The level of detected polymorphism varied from 66% when using primer 2224 to 100% when using primer 2242. The information content index of the PIC (polymorphism information content) primers varied in the range of 0.894-0.987. Analysis of genetic polymorphism revealed significant genetic variability among fungal isolates. Genetic analysis of amplification profiles of isolates of fungi of the genus Alternaria conducted using the GenAlex 6.5 software differentiated all isolates into 2 large groups. Isolates of A. infectoria were isolated in a separate cluster. Isolates of A. alternata and A. tennuissima were grouped in a different cluster depending on the species. Research results show that the iPBS method is highly effective for the genetic differentiation of phytopathogenic fungi at both intraspecific and interspecific levels.