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Vol 18, No 4 (2020)

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Genetic basis of ecosystems evolution
Induced expression of rolC for study of its effect on the expression of genes associated with nicotine synthesis in tobacco
Amini G., Sokornova S.V., Mohajjel-Shoja H., Stavrianidi A.N., Rodin I.A., Matveeva T.V.
Abstract

Background. Agrobacterium rhizogenes rol genes cause not only hairy root syndrome in plants, but also affect their secondary metabolism. There are cases of increasing of nicotine content in transgenic tobacco roots expressing rolC alone or in combination with other rol genes. In this work, we evaluated the change in the expression of nicotine synthesis genes and their regulators in response to the induction of expression of rolC.

Materials and methods. Plant material was represented by three Nicotiana tabacum genotypes: cv. Samsun and two transgenic lines, derived from this cultivar and containing rolC under dexamethasone inducible promoter: A. rhizogenes rolC (Pdex-A4rolC) and N. tabacum rolC (Pdex-trolC) correspondingly. Fluidigm Biomark RT-PCR was used for evaluation of expression of QPT1, QPT2, A622, ODC, ADC, PMT1, PMT2, PMT3, PMT4, MPO1, MPO2, BBL, MATE1, MATE2, ARF6, ERF168, ERF189, A4rolC, NtrolC, and reference gene gapdh. HPLC-MS / MS analysis was used to determine content of nicotine and its derivatives in plant tissues.

Results. Expression of PMT genes for the synthesis of the pyrrolidine ring, as well as the genes, controlling enzyme for final stages of nicotine synthesis, was higher in transgenic lines without induction of rolC expression. Regulatory genes were activated by dexamethasone in both transgenic and control lines, indicating the inapplicability of rolC dexamethasone induction for their study. The level of expression of PMT and MPO genes increased over time in transgenic dexamethasone-induced lines. Nicotine content decreased in transgenic dexamethasone-induced plants.

Conclusions. The rolC gene does not play a primary role in the regulation of nicotine synthesis genes. The mechanism of regulation of different nicotine biosynthesis genes and TFs varies.

Ecological genetics. 2020;18(4):413-422
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Assessment of variability of egg production traits based on analysis of SNP markers and search for traces of selection in the genome of Russian white chickens
Mitrofanova O.V., Dementieva N.V., Fedorova E.S., Pozovnikova M.V., Tyshchenko V.I., Shcherbakov Y.S., Plemyashov K.V.
Abstract

Objective. To assess the variability of egg production traits for nine SNPs, to search for traces of selection in the genome of Russian white chickens based on ROH patterns.

Methods. The material for the study was DNA isolated from the blood of Russian white chickens (n = 141). Nine SNPs associated with egg production at p < 5.16 · 10–5 according to GWAS data were selected for analysis. The frequencies of alleles and genotypes, the relationship between genotypes and characteristics of egg production were calculated, and ROH patterns were identified.

Results. Significant differences between genotypes were found in terms of age of laying the first egg (p < 0.005) and egg weight (p < 0.05). The genomic regions surrounding the target SNPs were analyzed according to the distribution of homozygous regions in them.

Conclusions. The substitutions rs317565390 and rs16625488 located in the 4.8–10.2 Mb region on chromosome 8 showed polymorphism, despite the fact that homozygous loci in this region of the genome are found in 58% of animals. For most SNPs, the prevalence of the frequency of one of the alleles was observed. As a cluster of increased selection pressure, a chick genome region in the 4.8–10.2 Mb region on chromosome 8 was identified.

Ecological genetics. 2020;18(4):423-432
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Grassflies of genus Meromyza (Diptera, Chloropidae) and grasses: the evolution of host plant preference
Safonkin A.F., Goryunova S.V., Goryunov D.V., Triseleva T.A.
Abstract

The present and literature data showed that Meromyza flies developed on grasses from 5 tribes: Poeae, Triticeae, Bromeae, Nardeae, Arundinarieae. The preference of host plants for 25, mainly Western Palaearctic species of Meromyza flies was analyzed: 11 species developed on grasses of the tribe Poeae, 4 – on Triticeae, 9 – on grasses from different tribes, 1 species developed on bamboo. A phylogenetic tree based on the mtDNA CO1 gene locus was constructed in the BEAST for 28 species of Meromyza flies, for 8 species of Drosophila and Campiglossa pygmaea. The host plants were known for 19 species Meromyza flies out of 28 studied species. An overview of the evolution of grasses is given. By the possible time of the genus Meromyza origin (not earlier than the middle of the Miocene), based on the known evolutionary scale of Drosophila, the Pooideae grasses had already been isolated and division into tribes occured. The features of non-specialized phytophage-oligophage (except M. acuminata) confirmed by the wide spectrum of host plants have been supposed for species close to ancestral haplotypes (M. nigriseta, M. pratorum, M. saltatrix, M. variegata) or representing independent branches in their clusters (M. acuminata, M. mosquensis, M. nigriventris). The differentiation of Meromyza genus with formation of new species with narrow oligophagy or monophagy was associated with adaptation to other wild grasses following the formation and increase in the abundance of “core pooids” (Triticodae + Poodae) grasses and the spread of herbal biomes in the Miocene. Oligophages M. nigriventris, M. nigriseta, M. variegata and monophages M. acuminata, M. grandifemoris damage cereal cultivars.

Ecological genetics. 2020;18(4):433-444
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Characterization of variability of the intergenic spacers cpDNA trnH–psbA, trnY–trnT AND rpoB–trnC in representatives of Pisum L. (Tribe Fabeae)
Dyachenko E.A., Semenova E.V., Kochieva E.Z.
Abstract

Background. Plant chloroplast genome have conservative structure, but its nucleotide sequence is polymorphous due to which cpDNA fragments are often used in taxonomic and phylogenetic studies. Despite the widespread distribution and use of Fabeae species, mainly peas (Pisum), data on the intraspecific diversity of cpDNA fragments are almost absent. The aim of the work was to analyze the intraspecific variability of three cpDNA spacers in Pisum.

Materials and methods. As a result of the work, intergenic spacers trnYtrnT, trnHpsbA and rpoBtrnC in 38 accessions of the Pisum and related Fabeae species were sequenced. Despite the fact that the selected chloroplast fragments are generally considered to be sufficiently variable in plants and are often used for phylogenetic studies, Pisum accessions have been found to have no intraspecific differences in two of the three spacers sequences analyzed.

Results and conclusion. A total 97 SNPs were detected in Pisum accessions, seven of them distinguished P. sativum from P. fulvum. The most variable of the analyzed fragments was the intergenic spacer rpoB–trnC. Based on rpoB–trnC sequence 17 haplotypes in P. sativum and four haplotypes in P. fulvum were revealed. The cpDNA sequencing data were used for a phylogenetic analysis. On the obtained tree Vavilovia formosa accession formed a separate branch from pea accessions. All Pisum accessions fall in one cluster, split into distinct P. sativum and P. fulvum subclusters (BI = 99%).

Ecological genetics. 2020;18(4):445-456
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Genome destabilization under stress in cells of the prefrontal cortex, hippocampus and bone marrow of rats with contrast excitability of the nervous system
Pavlova M.B., Vaido A.I., Khlebaeva D.A., Daev E.V., Dyuzhikova N.A.
Abstract

We studied changes in the stability of the genome in cells of two brain regions (prefrontal cortex and hippocampus), as well as in the bone marrow of rats with a hereditary high and low thresholds of excitability of the nervous system (strains HT and LT, respectively) after prolonged exposure with emotional-pain stressor. To study the reactivity of the brain cells genome, phosphorylated histone γ-H2AX (γ-H2AX phospho Ser139) was used. The level of mitotic disturbances in bone marrow cells was also assessed. Between the animals of the control groups, there were no interstrain differences in the studied parameters. Stress exposure increases the immunoreactivity to γ-H2AX phospho Ser139 of the prefrontal cortex cells and the level of chromosomal aberrations in bone marrow cells in animals of both strains. In cells of the dentate gyrus of the hippocampus, a specific increase in immunoreactivity to γ-H2AX phospho Ser139 was revealed in rats of the low-excitable HT strain. The relationship between the reaction of cells of this zone of hippocampus to the stressor exposure with the hereditary level of excitability of the nervous system of animals is discussed.

Ecological genetics. 2020;18(4):457-466
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Application of small RNAs for plant protection
Tretiakova P.Y., Soloviev A.A.
Abstract

Double-stranded small RNAs (dsRNA) perform various regulatory functions via RNA-interference. Additionally, they can be transported between various plant species and their pathogens and pests via extracellular vesicles, protecting RNA from nucleases. Plants secrete short dsRNA molecules to defend themselves against pathogens. The latter also use small RNAs when infecting crops. Some dsRNAs of pathogens are known as “ribonucleic effectors”. Host-induced gene silencing (HIGS) was shown to be effective when breeding resistant varieties and analyzing plant-pathogen interactions. However, complexity of transgenesis and society fear of genetically modified products make HIGS application difficult. The appearance of a new strategy based on plant spraying with dsRNA gave a new perspective of plant protection. Currently such a strategy requires accurate studying as well as the development of efficient systems stably producing high-quality dsRNA.

Ecological genetics. 2020;18(4):467-482
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Genetic toxicology
Cytogenetic effects in the needles intercalar meristem of Japanese red pine in the remote period after the Fukushima NPP accident
Vasiliev D.V., Geraskin S.A., Yoschenko V.I., Lychenkova M.A., Nanba K.
Abstract

Background. The study of the long-term effects of chronic radiation exposure on plants and animals, which are still the subject of scientific discussion, is necessary to understand the consequences of radiation accidents. After the Fukushima nuclear power plant accident, some of the young pines and spruces showed an increased frequency of apical dominance cancelling. The most probable cause of the observed morphoses is associated with damage to the apical meristem of coniferous plants by radiation in the first year of the accident, when they received the highest absorbed doses. If this hypothesis is true, then even 8 years after the accident it will be possible with high degree of probability to detect an increased level of cytogenetic abnormalities in the intercalary meristem of needles of plants from these populations.

The aim of this work was to verify this hypothesis.

Materials and methods. Five populations of Japanese red pine from territories contaminated with radionuclides as a result of the accident at the Fukushima nuclear power plant were investigated. The frequency and spectrum of cytogenetic abnormalities in the intercalary meristem of needles were determined by the ana-telophase analysis.

Results. The frequency of aberrant cells in the needles intercalary meristem of Japanese red pine from the contaminated with radionuclides territory statistically significantly exceeds the control level in all impact sites and increases along with the dose rate. Although there is no correlation between the frequency of cytogenetic abnormalities in needles and the presence of cancellation of apical dominance in plants, all pine populations from radioactively contaminated territories are characterized by an increased frequency of both cytogenetic abnormalities and morphoses associated with the cancellation of apical dominance.

Conclusion. Radiation damage to the apical meristems of conifers in the first year of the accident, when they received the highest absorbed doses, is the most likely cause of the increased frequency of cancellation of apical dominance in the studied populations of Japanese red pine from the zone affected by the accident at the Fukushima nuclear power plant.

Ecological genetics. 2020;18(4):483-492
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Methodology in ecological genetics
Environmental DNA: history of studies, current and perspective applications in fundamental and applied research
Pinakhina D.V., Chekunova E.M.
Abstract

This review article is dedicated to a relatively young, actively developing approach to biodiversity assessment – analysis of environmental DNA (or eDNA). Current views on the nature of eDNA, a brief overview of the history of this approach and methods of eDNA analysis are presented. Major research directions, utilizing eDNA techniques, and perspectives of their application to the study of biodiversity are described. Key issues in development of eDNA approach, its advantages and drawbacks are outlined.

Ecological genetics. 2020;18(4):493-509
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