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Vol 22, No 3 (2024)

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Genetic basis of ecosystems evolution

Effect of mutations in the Sym7, Sym19 and Sym34 genes on the interaction of pea (Pisum sativum L.) with the arbuscular mycorrhizal fungus Rhizophagus irregularis

Shtark O.Y., Zhernakov A.I., Kichigina N.E., Akhtemova G.A., Sulima A.S., Zorin E.A., Zhukov V.A.

Abstract

BACKGROUND: Within the pea (Pisum sativum L.) species, genotypes with high and low responsiveness to inoculation with arbuscular mycorrhizal fungi can be distinguished.

AIM: The aim of this study was to test the hypothesis that pea responsiveness to arbuscular mycorrhizal fungi inoculation may be inversely correlated with root colonization levels.

MATERIALS AND METHODS: The wild-type line Finale with low responsiveness to arbuscular mycorrhizal fungi inoculation and symbiotic mutants obtained on its basis were used. Plants were grown under controlled climatic conditions with a deficiency of available phosphorus; the fungus Rhizophagus irregularis was used for inoculation. Parameters of plant growth and development of reproductive organs were determined 52 and 71 days after inoculation, which corresponded to the flowering and pod filling stages, respectively.

RESULTS: All mutant lines under conditions without inoculation had generally reduced parameters compared to the original line Finale. Inoculation led to a decrease in many parameters in the line Finale. Mutations in the Sym7 and Sym34 genes, which led to a decrease or delay in the start of mycorrhization, respectively, contributed to the manifestation of a positive plant response to inoculation. The mutant in the Sym19 gene almost completely lacked intrartadical colonization, while inoculation had no effect on the growth and development of above-ground organs.

CONCLUSIONS: The study results support the idea that reducing mycorrhization levels can have a positive effect on pea plants.

Ecological genetics. 2024;22(3):225-242
pages 225-242 views

Genetic diversity of naked barley accessions from the VIR collection for resistance to powdery mildew in the North-West Region of the Russian Federation

Lukina K.A., Abdullaev R.A., Alpatieva N.V., Loskutov I.G., Kovaleva O.N.

Abstract

BACKGROUND: Barley is an important grain crop characterized by adaptability to various growing conditions. In recent years close attention has been paid to groups of naked barley which compared to covered barley is more susceptible to the influence of pathogens, that decreases the yield and quality of grain. Powdery mildew is the most harmful diseases of barley (caused by the biotrophic fungus Blumeria graminis (DC.) Golovin ex Speer f. sp. hordei Marchal). The search for new promising sources of resistance to powdery mildew is necessary for barley breeding.

AIM: The aim is studying the powdery mildew resistance of naked spring barley accessions from the world collection of VIR and identifying promising sources for economically valuable traits.

MATERIALS AND METHODS: In field and laboratory conditions 271 of naked barley accessions of different ecological and geographical origin were studied for powdery mildew resistance and other economically valuable traits (lodging resistance, duration of the vegetative period, yield). The pathogen inoculum for laboratory work was represented by the north-western population of the pathogen. The resistance of barley samples was assessed in the field using the VIR point scale, in the laboratory using the E.B. Mains, S.M. Dietz point scale. The highly effective to powdery mildew resistance allele mlo11 was identified using PCR.

RESULTS: The diversity of barley of different origins in resistance to powdery mildew is shown. 16 samples mainly from Europe, local forms from Ethiopia, Japan and India, were found to be resistant in field condition. According to the results of the assessment at the juvenile stage, 1 highly resistant sample k-31058 and 5 moderately resistant (k-20923, k-25801, k-27165, k-29911, k-30231) were identified. The naked forms k-20923 from Germany and k-29911 from Poland were resistant at all stages of plant development. The mlo11 allele was detected in the Arabische variety (k-20923) and heterogeneous pathogen resistance accessions k-20921, k-25793, k-27080, k-29440, k-29820.

CONCLUSIONS: As a result of the work the sources of resistance to powdery mildew with a complex of economically valuable traits were identified, which can be involve in the breeding.

Ecological genetics. 2024;22(3):243-253
pages 243-253 views

Human ecological genetics

Association of superoxide dismutase and catalase genetic variants and their gene-gene interactions with the severity of COVID-19

Eid M.A., Aleksandrova A.A., Kosenko P.O., Shkurat T.P.

Abstract

BACKGROUND: Since the outbreak of COVID-19 infection, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), oxidative stress has been proposed as an important player in its severity. This increased the interest in studying antioxidant systems to evaluate their possible role in counteracting disease progression.

AIM: The aim of the current study was to investigate the association of single nucleotide polymorphism (SNP) of superoxide dismutase (SOD) and catalase (CAT) genes with the severity of COVID-19.

MATERIALS AND METHODS: Study subjects were divided into two groups based on the severity of their symptoms. Allele-specific PCR was used for genotyping, and multifactor dimensionality reduction (MDR) analysis was performed to investigate the SNP–SNP interaction models.

RESULTS: The results showed a significant association of SOD2 rs4880 with the severity of COVID-19 (p = 0.002). SOD2 47TT genotype was significantly more frequent among patients with severe COVID-19 (OR 4.34; 95% CI 1.72–10.96). The three-locus SNP–SNP interaction model, resulted from MDR analysis, was statistically significant (0.55 × 10–4, OR 3.81; 95% CI 1.96–7.42). Carriers of SOD1 7958G * SOD2 47T * CAT 262C allele combination had a higher risk of severe COVID-19 (p = 0.0045, OR 2.84, 95% CI 1.40–5.78).

CONCLUSIONS: The obtained results contribute to better understanding of COVID-19 pathogenesis and suggest novel potential prognostic biomarkers of the infection.

Ecological genetics. 2024;22(3):255-264
pages 255-264 views

Genome-wide epigenetic changes in compartments of genetically unbalanced human blastocysts

Tikhonov A.V., Krapivin M.I., Malysheva O.V., Koltsova A.S., Komarova E.M., Golubeva A.V., Efimova O.A., Pendina A.A.

Abstract

BACKGROUND: Epigenetic genome reprogramming is an important determinant of human embryo development. However, its mechanisms remain poorly elucidated, especially in genetically unbalanced embryos.

AIM: The aim of this study is the analysis of DNA methylation and hydroxymethylation levels in trophectoderm and inner cell mass of genetically balanced and unbalanced human blastocysts.

MATERIALS AND METHODS: Twenty-two IVF-derived human blastocysts were enrolled in the study; of these blastocysts, 15 were genetically unbalanced and 7 — genetically balanced. Detection of 5-methylcytosine and 5-hydroxymethylcytosine was performed on trophectoderm and inner cell mass nuclei by indirect immunofluorescence.

RESULTS: In genetically unbalanced blastocysts, the DNA methylation level was elevated in both compartments. The DNA hydroxymethylation level, in contrast, was elevated only in inner cell mass, whereas trophectoderm cells retained the same level as in genetically balanced embryos. These changes equalized the inner cell mass and trophectoderm DNA hydroxymethylation levels in genetically unbalanced blastocysts, while in genetically balanced ones the 5-hydroxymethylcytosine content in inner cell mass lagged behind that in trophectoderm.

CONCLUSIONS: Genetic imbalance is associated with differential epigenetic changes in trophectoderm and inner cell mass cells of human blastocysts: DNA methylation level increases in both compartments while DNA hydroxymethylation level increases only in inner cell mass. The trophectoderm cells in genetically unbalanced blastocysts retain the same hydroxymethylation level as in genetically balanced ones, suggesting a possible explanation of the ability of karyotypically abnormal embryos to implant.

Ecological genetics. 2024;22(3):265-276
pages 265-276 views

Populations of the Caucasus as an object for studying the process of adaptation to conditions of high-altitude hypoxia

Dzhaubermezov M.A., Ekomasova N.V., Mustafin R.N., Chagarov O.S., Fedorova Y.Y., Gabidullina L.R., Nurgalieva A.K., Prokofyeva D.S., Khusnutdinovna E.K.

Abstract

The work examines the main mechanisms responsible for the process of acclimatization of the population of high mountain regions to the conditions of hypobaric hypoxia. The purpose of this review is to describe the pathways of genetic, epigenetic and physiological control in the adaptation of indigenous populations of highlands to reduced barometric pressure and oxygen tension in the environment. It has been shown that populations living in different high-mountain regions demonstrate different ways of adaptation in response to a decrease in the partial pressure of oxygen in the inspired air. The changes that occur in the body in response to stressful conditions are extremely diverse. These include changes in the respiratory, cardiovascular, hematological systems and cellular adaptation. In this review, we examine genomic variations leading to evolutionary adaptation to life at high altitudes, gene expression, pathophysiological and metabolic features, and long-term adaptation in various high-altitude populations. We also consider the peoples of the Caucasus as one of the most promising populations for further study of complex adaptation mechanisms.

Ecological genetics. 2024;22(3):277-292
pages 277-292 views

Methodology in ecological genetics

Optimization of transformation conditions of the yeast Saccharomyces cerevisiae to determine coregulators of the transcription factor NIN in a yeast two-hybrid system

Dymo A.M., Kantsurova E.S., Dolgikh A.V., Dolgikh E.A.

Abstract

BACKGROUND: The method of protein-protein interaction analysis using the yeast two-hybrid system in Saccharomyces cerevisiae cells is used to search for protein coregulators. This method is also used for mass screening of libraries of cloned fragments of complementary DNA (cDNA) that are translated in the cell. The key factor in the success of such screening is the level of efficiency of yeast cell transformation, since the resolution of the analysis is based on this.

AIM: The aim of this study is to search for optimal parameters for chemical transformation of yeast cells to increase the resolution of cDNA library screening.

MATERIALS AND METHODS: Plasmids pDEST22 and pDEST32 were used for chemical transformation of the yeast strain S. cerevisiae pJ69-4A. For screening, a cDNA library was used, obtained on the basis of mRNA isolated from the roots of pea Pisum sativum cultivar Finale, inoculated with rhizobia.

RESULTS: Factors influencing the efficiency of transformation were identified. Among them are the molecular weight of polyethyleneglycol used for transformation, as well as the number of cell division cycles that the culture undergoes. The effect of the number and size of plasmids used in transformation was also shown. Using the optimized protocol, a cDNA library was successfully screened to find coregulators of the NIN transcription factor.

CONCLUSIONS: Based on the data obtained, optimal parameters were determined that allow achieving a high level of competence in yeast cells. The use of the described protocol allowed for successful screening of the library to identify coregulators of the NIN transcription factor.

Ecological genetics. 2024;22(3):293-306
pages 293-306 views