


Том 60, № 8 (2024)
ОБЗОРНЫЕ И ТЕОРЕТИЧЕСКИЕ СТАТЬИ
Genome-Wide Analysis in the Study of the Fetal Growth Restriction Pathogenetics
Аннотация
Fetal growth restriction is a complication of pregnancy that defined as the inability of the fetus to realize its genetically determined growth potential. Despite the high social and medical significance of this problem the exact pathogenesis of fetal growth restriction is not known by now. Therefore, the analysis of the molecular genetics mechanisms of this pathology within the framework of approaches using modern high-performance technologies of next generation sequencing is of undoubted interest. In this review we focused on the analysis of data obtained in studies of the fetal growth restriction genetics component. The authors of these researches used next generation sequencing technologies and carried out whole transcriptome profiling. The results of the genes expression genome-wide analysis in placental tissue allow us to identify 1430 differentially expressed genes between fetal growth restriction and normal pregnancy, of which only 1% were found in at least two studies. These differentially expressed genes are involved in the Wnt/β-catenin signaling pathway that plays an important role in cell migration, neural pattern formation and organogenesis during embryonic development. Common genes are associated with both obstetric and gynecological diseases, as well as with various somatic conditions from the groups of neurodegenerative, cardiovascular diseases and mental disorders, which probably reflects their involvement in the development of postnatal consequences of fetal growth restriction. The results of our work don‘t point only to potential molecular mechanisms and key genes underlying fetal growth restriction, but also indicate the important role of gene-gene communications in this pathology implementation: about 30% of all identified differentially expressed genes products interact with each other within the same gene network. In general, genome-wide RNA sequencing combined with the analysis of protein-protein interactions represents a promising direction in research on the development and functioning of the placenta, as well as the identification of placental insufficiency diseases genetics mechanisms, including fetal growth restriction.



ГЕНЕТИКА МИКРООРГАНИЗМОВ
Molecular Genetic Characteristics of the Mutant Strain B-162/2 of the Bacteria Pseudomonas chlororaphis subsp. aurantiaca
Аннотация
The production of microorganisms that produce biologically active compounds for agriculture, the chemical, veterinary and pharmaceutical industries as well as for environmental protection continues to be an important direction of microbial biotechnology. One of the most effective approaches to the production of producers is chemical mutagenesis, which, in combination with the right breeding strategy, makes it possible to obtain highly productive strains. A significant disadvantage of chemical mutagenesis is the large number of induced mutations in the genomes of mutant strains, which makes it difficult to identify genes and, accordingly, biosynthetic pathways involved in the production of a given compound. The solution to this problem is modern technologies of genome sequencing and analysis, which make it possible to identify new genes and unknown biochemical pathways involved in the formation of biologically active compounds. The aim of the work was to analyse the genome of the mutant strain B-162/2 of the bacterium Pseudomonas chlororaphis subsp. aurantiaca, which is capable of increased production of biologically active compounds of the phenazine series and is resistant to hydrogen peroxide. When analysing the genome of strain B-162/2 in full size, 6482 coding sequences and 64 coding RNA sequences were identified. Comparison of the genome of the B-162/2 strain with the genome of the wild type B-162 allowed the identification of 39 mutations, 5 of which are localised in intergenic regions, and 34 affected coding sequences. Of the mutations detected, 14 led to a radical amino acid substitution in the proteins and 2 led to the formation of premature stop codons (methyl group sensor and MFS-type transporter). Several substitutions with high values of the Grantham coefficient were found, which could possibly lead to a change in the activity of the proteins concerned. The presence of three regions with phage genes in the genome of the B-162/2 strain was detected.



ГЕНЕТИКА РАСТЕНИЙ
Differentiation and Taxonomic Identification of Roburoid Oaks in the Caucasian and Crimean Regions Using Nuclear Microsatellite Markers
Аннотация
The inter- and intra-specific structure of genetic variability was studied using 18 microsatellite loci (nSSRs) in closely related roburoid oaks in the Crimean-Caucasian region.The seven most widespread Quercus taxa in the region were studied in 29 morphologically pure populations from different parts of the North Caucasus, Transcaucasia, Crimea and northeastern Europe. Most taxa were studied using nSSR markers for the first time. Among the 492 trees studied, Bayesian clustering method implemented in STRUCTURE identified clusters corresponding to the pedunculate oak Quercus robur, the Hartwiss oak Q. hartwissiana, the Caucasian oak Q. macranthera, the downy oak Q. pubescens and three subspecies of sessile oak: Q. petraea ssp. petraea, Q. petraea ssp. iberica, Q. petraea ssp. medwediewii. Geographic structure was identified within Q. robur, Q. pubescens and Q. p. ssp. petraea. The 18 nSSR loci used are efficient in the taxonomic assignment of individuals, and identifying hybrids. The close relationship between the “long-pedunculate” roburoid oaks (Q. robur and Q. hartwissiana) is shown, with a greater difference from other species. For one of the subspecies of sessile oak, widespread in the North Caucasus and Crimea Q. petraea ssp. medwediewii (syn. Q. calcarea), or limestone oak, significant differences from other taxa were found, reaching the species level. The assumption of a possible hybrid origin of this taxon as a result of hybridization of Q. petraea and Q. pubescens is not confirmed by genetic analysis. The other two subspecies of Q. petraea (Q. p. ssp. petraea and Georgian oak Q. p. ssp. iberica) are differentiated to a lesser extent and are related to each other, which confirms the legitimacy of distinguishing two geographically isolated taxa at the rank of subspecies. The highest variability was observed in Q. pubescens (He = 0.777). In Q. p. ssp. medwediewii variability was lower than in other widespread taxa (He = 0.652), and was approximately at the level of variability of Q. hartwissiana (He = 0.633) and Q. macranthera (He = 0.659). Clear differentiation of taxa by nuclear markers shows the limited introgression in closely related oak species in the Caucasus and Crimea. The identified genetic clusters can be used as reference groups for further population genetic studies of oaks in the Crimean-Caucasian region.



ГЕНЕТИКА ЖИВОТНЫХ
Calpastatin CAST and Androgen Receptor AR Gene Polymorphism Studyas Meat Quality Predictors in Reindeer Rangifer tarandus
Аннотация
Marker-based selection on reindeer meat productivity is in the early stages of development, which requires the study of variability in candidate genes for meat productivity. We chose the calpastatin and androgen receptor genes as such genes to study. Polymorphisms and indels in the androgen receptor gene have been associated with height and weight characteristics in different domesticated animal species. Variation in the region of the calpastatin CAST gene, according to the results of many studies, has been associated with meat quality and meat productivity of livestock. Principal component analysis of CAST variability has grouped together wild and domestic deer from Yakutia, as well as wild and domestic deer from the Amur region, which implies gene flow between local breeds of domesticated deer and wild populations. Moreover, in the case of three microsatellite loci found in this study in the intron of the androgen receptor, principal component analysis separated wild and domestic deer.



Analysis of the Genetic Structure of 29 Horse Breeds of Russian Selection by str Markers
Аннотация
The current stage of genetic certification of horses of factory and local breeds based on microsatellite analysis makes it possible to quite effectively carry out identification and genetic examination of the origin of breeding animals, as well as solve the problem of assessing and preserving genetic resources. With a reduction in the number of breeding stock to 200–300 mares, observed in a number of breeds, the threat of a decrease in the genetic diversity of populations and the accumulation of genetic load increases, which necessitates the need to study and monitor the genetic structure of horse breeds. In this regard, our comparative genetic analysis of polymorphism of 17 microsatellite loci in 20541 horses of 30 factory and local breeds allows us to certify the basic part of the genetic resources of the horse breeding of the Russian Federation. including riding, trotter, draft and local breeds. During the genetic population analysis of the studied breeds, basic parameters were assessed: the total number of allele variants (Na), the effective number of alleles (Ae), the average number of alleles per locus (MNA), the level of observed (Ho) and expected heterozygosity (He), as well as the coefficient of intrapopulation inbreeding Fis. Phylogenetic relationships of breeds were assessed using the R and R Studio software packages. Among horse breeds of different specializations, the highest values of all indicators of genetic diversity (Ae, Ho, He and Na) were determined in aboriginal populations. In the allele pool of local horse breeds, there were rare alleles ASB2T, HMS7S, HMS6J, HMS6H, HMS2T, HMS1O, HTG7L, HTG6L, HTG6H, VHL20S, ASB17Z, ASB17X, ASB17U, LEX3S, LEX3R and CA425E, which were absent in horses of factory breeds. Among the riding horse breeds created in Russia, the Budennovsk, Don and Kabardian horse breeds stood out due to the presence of rare alleles. Alleles ASB2G, ASB2F, HMS2F, HTG7Q and ASB23O were found in trotter horses, which were not identified in the genetic structure of other breeds. The phylogenetic analysis showed the division of horse breeds into two clear subclusters, the first of which included only factory breeds. The second cluster united all the native breeds, as well as the Orlov trotter and a group of draft breeds, which were used for many years as improvers of the local horse population. The analysis of the genetic structure of domestic horse breeds revealed a fairly high reserve of diversity even in small populations, which is an indispensable condition for successful selection in horse breeding.



Polymorphism of Russian Populations of Rhopalosiphum padi L. Based on DNA Markers
Аннотация
Using the next-generation sequencing (NGS) technology, the nucleotide polymorphism in a fragment of the ND4 gene encoding NADH dehydrogenase subunit 4 was studied in 14 samples from three populations of the bird cherry-oat aphid (Rhopalosiphum padi L.) and the range of nucleotide polymorphism was determined. The insects were collected in 2021 and 2022 in the North-West of Russia (in the vicinity of St. Petersburg) and in the northern Caucasus (Krasnodar Territory and Dagestan). Mitochondrial DNA haplotypes were identified, which have 97.95–99.80% sequence identity with the reference GenBank accession number KT447631.1. The level of intraspecific polymorphism of a 438 bp ND4 gene fragment in Rh. padi varied from 0.2 to 4.3%. In the two-year experiments, 33 polymorphic sites (17 transitions and 16 transversions) were found in the ND4 sequences, which made it possible to identify 30 mitochondrial DNA haplotypes. The Rh. padi populations collected simultaneously on different host plants or at different times on bird cherry (spring) and cereals (summer) differed in the proportion of the main haplotype, as well as in the composition of unique minor haplotypes. Analysis of the ratio of mitochondrial DNA haplotypes suggests the important role of the host plant genotype in the formation of the structure of Rh. padi populations.



ГЕНЕТИКА ЧЕЛОВЕКА
Study of a Polymorphic Variant of the Cold Receptor Gene Trpm8 (rs7593557) in 15 Populations of the Altai-Sayan Region and the Far East
Аннотация
The thermoreceptor gene TRPM8 (rs7593557) was analyzed in 15 population samples living in different regions of Northern Asia, the Altai-Sayan Highlands and Canada. High frequencies of a rare genotype and allele in the populations of the Altai-Sayan region and Western Siberia were found among the Telengits (22.2 and 41.7% respectively), low among the Siberian Tatars (3.2 and 18.5% respectively), and among the peoples of northern Siberia and the Far East high frequency was found among the Nanais (22.2 and 42.6% respectively), and a low frequency among the Yakuts (1.1 and 10.9% respectively). No deviations from Hardy-Weinberg equilibrium were found. Trans-association of TRPV1, TRPA1 and TRPM8 gene polymorphisms was carried out using the regression analysis method in 14 populations. Of all three pairs, only one, TRPV1/TRPM8, showed a positive correlation (0.55, df = 13, P-value – 0.032). In pairs TRPV1/TRPA and TRPA1/TRPM8, a negative correlation was revealed (–0.545, df = 13, P-value – 0.048) and (–0.46, df = 13, P-value – 0.097) respectively. Our data indicate that the studied polymorphisms of the TRPV1 and TRPM8 genes are correlated with each other and negatively correlated with TRPA. The results obtained may indicate the coevolution of these genes. It was previously shown that TRPV1, as well as TRPM8, was detected with high frequency in the Nanai population. It is likely that these two mutations came simultaneously from East Asia and spread throughout Russia, which explains the fact that they are positively correlated with each other.



The Role of Gene-Gene Interactions in the Formation of Predisposition to Preeclampsia
Аннотация
Identification of the hereditary basis of preeclampsiaremains a relevant area for medical genetics. Despite numerous attempts to search for the main predetermining factors due to the multifactorial nature of the preeclampsia no generally accepted hypotheses for the pathogenesis of this pregnancy complication. One of the progressive approaches to the study of complex diseases is a analysis of gene-gene interactions which makes it possible to isolate from a large array of combinations factors that can determine a high or low risk of predisposition within the pathology under consideration. In the presented work the analysis of gene-gene interactions was used to create a model that predicts the risk of severe preeclampsia and find key combinations of genes predisposing to the development of preeclampsia in the Russian population were obtained.For the first time was demonstrated the prognostic potential of combinations of the rs3774298 BCL6 and rs2071045 LEP loci in the development of a severe form of preeclampsia (OR = 2.97). Additionally it was found that the rs3774298 polymorphic variant of the BCL6 gene is localized in a functionally active region of the genome, located in the binding site of the transcription factor CTCF, which can function as both a transcription activator and a repressor. That emphasizes the role of cell regulatory systems in the mechanisms of the formation and course of preeclampsia.



Similarity of Human Mitochondrial DNA Nucleotide Substitution Spectra Reconstructed Over One and Many Generations
Аннотация
Using phylogenetic analysis of mitochondrial whole genome nucleotide sequences (mtDNA), allowing the study of genetic changes over many generations, a spectrum of nucleotide substitutions (along the L-strand of mtDNA) was reconstructed in European populations. The spectra of mtDNA nucleotide substitutions observed in a heteroplasmic state (at ≥1% and ≥5% levels) in first generation children were also analyzed. It was found that the spectra of nucleotide substitutions reconstructed over one and many generations do not differ practically in the main parameters: the distribution of pyrimidine and purine substitutions (with predominance of transitions T>C), the ratio of the number of transitions and transversions. Analysis of the phylogenetic tree of mtDNA haplotypes in Europeans clearly revealed the influence of negative (purifying) selection on mitochondrial gene pools. It is suggested that the selective processes guiding the mtDNA evolution in one and many generations are of a similar nature, i.e., caused by negative selection. The problem of how mutations occur and spread in mitochondria of germ line cells is discussed.



Dynamics of the Population Structure of the South of Central Russia Over a 130-Year Period. Migration Processes
Аннотация
This article assesses the dynamics of indicators characterizing marriage and migration parameters among the population of the south of Central Russia from 1890 to 2018. In the structure of marriages over the 130-year period, there was a significant decrease (1.6–2.2 times) in the share of isolocal marriages and a significant increase the share of heterolocal marriages (almost 11 times), while the size of the elementary population increased from the village level to the district/region level. From 1890 to 2018 the dynamics of isolocal marriages are more pronounced among the urban populationn and the dynamics of heterolocal marriages are more pronounced among rural residents. Over the 130-year period positive marital assortativity by place of birth of spouses decreased by 1.5 times without significant differences in the level and dynamics of marriage selectivity by place of birth of spouses between the urban and rural populations (except for the period 1951–1953). A strong direct correlation was established between the level of marital assortativeness and the share of marriages concluded within one region and one district (r = 0.90, p < 0.05) and a negative one – on the share of heterolocal marriages (concluded between immigrants from different regions) (r = −0.90, p < 0.05).



КРАТКИЕ СООБЩЕНИЯ
Sequencing and Annotation of the Chloroplast Genome of Triticum militinae – a “Natural Mutant” of Tetraploid Wheat Triticum timopheevii Zhuk.
Аннотация
Triticum militinae Zhuk. et Migusch. – tetraploid wheat with the GAA genome, considered a natural naked mutant of T. timopheevii Zhuk. Previously, experiments were conducted for this wheat to study the karyotype and crossing characteristics. To clarify its origin and relationship with other representatives of the wheat family, analysis of the chloroplast genome of T. militinae, which has previously remained unstudied, is of great interest. The sucrose gradient method was used to isolate chloroplast DNA from leaves. Sequencing was performed using the FASTASeq 300 Sequencing Kit V1.0 100 M reads/flow cell on a Genolab M sequencer (GeneMind, China). For the first time, we sequenced and annotated the complete chloroplast genome of T. militinae with a size of 135898 bp. In the structure of the plastid genome there are a pair of inverted repeats with a size of 21552 bp each, the region of a small single copy (SSC) – 12791 bp and the region of a large single copy (LSC) – 80003 bp. As part of the chloroplast genome of T. militinae 132 structural genes were found, of which 85 protein-coding genes, 31 tRNAs and 4 rRNA genes.



Genetic characteristics of the Gray Mountain Caucasian Bee Apis mellifera caucasica
Аннотация
In this study we present the results of a comparative genetic analysis of bees of the Apis mellifera caucasica subspecies with the subspecies A. m. carnica and A. m. mellifera. We performed polymorphism analysis of nine microsatellite loci (Ap243, 4a110, A24, A8, A113, A88, Ap049, A28, and A43) and determined the haplotypes of the tRNAleu-COII locus. Analysis of the genetic structure of representatives of three subspecies of honey bees, widespread in Russia, showed a significant level of their differentiation even when using a small set of microsatellite loci. An assessment of the prevalence of tRNAleu-COII haplotypes in the three studied samples showed that for A. m. caucasica the predominant haplotype was C2j.


