Russian Journal of Genetics最新文献

Abstract—Using phylogenetic analysis of mitochondrial whole genome nucleotide sequences (mtDNA), which allows 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 the ≥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 practically do not differ in their main parameters: the distribution of pyrimidine and purine substitutions (with predominance of T→C transitions) and 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., are caused by negative selection. The problem of how mutations occur and spread in mitochondria of germ line cells is discussed.

Abstract—Fetal growth restriction is a complication of pregnancy that is 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. 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 genetics component of fetal growth restriction. The authors of these studies used next generation sequencing technologies and carried out whole transcriptome profiling. The results of the gene 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, which 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 do not only point to potential molecular mechanisms and key genes underlying fetal growth restriction, but also indicate the important role of gene–gene communications in this pathology: 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 in the development and functioning of the placenta, as well as the identification of genetic mechanisms of placental insufficiency diseases, including fetal growth restriction.

Abstract—

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 in the share of heterolocal marriages (by 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 was more pronounced among the urban population and the dynamics of heterolocal marriages was 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 of 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).

Abstract—Identification of the hereditary basis of preeclampsia remains 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 exists. One of the progressive approaches to the study of complex diseases is an analysis of gene–gene interactions, which makes it possible to isolate factors that can determine a high or low risk of predisposition within the pathology from a large array of combinations. In the presented work, 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 one to the development of preeclampsia in the Russian population. For the first time 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) was demonstrated. Additionally, it was found that the rs3774298 polymorphic variant of the BCL6 gene is located 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. This emphasizes the role of cell regulatory systems in the mechanisms of the formation and course of preeclampsia.

Abstract

Hemicentrotus pulcherrimus is an important commercial aquatic species. However, wild stocks have dramatically decreased in recent decades, and the gonads of H. pulcherrimus of different sexes showed significant differences in gonad index, gonad color, and flavour. Understanding the population genetic structure and sex-differentiation/determination mechanism can provide vital information for genetic conservation and improvement. In the present study, the SuperGBS method was used to identify genome-wide SNPs from a collection of 80 individuals consisting of four geographical populations covering the natural habitats of H. pulcherrimus in China seas. A total of 5785 high-quality SNPs were detected by using SuperGBS technology. The genetic diversity index showed that all populations had similar patterns with high F_is and low N_e, suggesting that it is necessary to carry out the conservation of H. pulcherrimus in China. Low genetic differentiation among the four geographical populations was detected by pairwise F_st, PCA, and admixture analysis. In addition, three sex-related SNPs located on three scaffolds were identified, suggesting a ZW-ZZ sex determination system in H. pulcherrimus. However, no sex-specific marker was identified in this study. Therefore, larger sample sizes and marker numbers need to be implemented to investigate the sex-associated markers and genes of H. pulcherrimus. In general, this study provides a molecular basis for population genetic structure and sex-differentiation/determination mechanism of H. pulcherrimus.

Abstract

The Ib River is an important tributary of the Mahanadi River. The aim of the present study was to establish a reliable barcoding reference database for fish in Ib River. A total of 134 specimens, belonging to 42 species within 32 genera, 18 families, and 11 orders, were subjected to PCR amplification of the target region of mitochondrial genome and sequenced. The average length of the 134 barcodes was 648 bp. The average K2P distances within species, genera, and families were 0.13, 9.94, and 16.79%, respectively. The average interspecific distance was approximately 76.46 times higher than the mean intraspecific distance. The Barcode Index Number (BIN) discordance report showed that 134 specimens represented 42 BINs, of which 13 were singletons, 29 were taxonomically concordant while no species taxonomically discordant in our dataset. The barcode gap analysis demonstrated that 100% of the fish species examined could be discriminated by DNA barcoding. These results provide new insights into fish diversity in the Ib River and can provide a basis for the development of further studies on fish fauna.

Abstract—

The TRPM8 thermoreceptor gene (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) and were low among the Siberian Tatars (3.2 and 18.5% respectively), while 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 the 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 TRPV1/TRPA and TRPA1/TRPM8 pairs 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.

Abstract—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 that are 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.

Abstract

The inter- and intra-specific structure of genetic variability was studied using 18 microsatellite loci (nSSRs) in closely related roburoid white 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-peduncle” 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 inter-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 durmast 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 (H_e = 0.777). In Q. p. ssp. medwediewii variability was lower than in other widespread taxa (H_e = 0.652), and was approximately at the level of variability of Q. hartwissiana (H_e = 0.633) and Q. macranthera (H_e = 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.

Abstract—

Marker-assisted selection for improving reindeer meat production is at the early stages of development, which requires analysis of variation within the candidate genes for meat production. The calpastatin and androgen receptor genes were chosen as such genes to study their variability in reindeer. In different domesticated animal species, polymorphisms and indels in the androgen receptor gene were associated with growth and weight characteristics. Based on the results from many studies, sequence variation in the calpastatin CAST gene region was associated with meat quality and meat production of livestock. Principal component analysis of CAST variability grouped wild and domestic deer from Yakutia, as well as wild and domestic deer from Amur oblast, which implies gene flow between local breeds of domesticated deer and wild populations. At the same time, in the case of three microsatellite loci found in the present study in the intron of the androgen receptor gene, principal component analysis separated wild and domestic deer.