Showing papers in "Russian Journal of Genetics in 2020"

Regulatory Mechanism of Maize ( Zea mays L.) miR164 in Salt Stress Response

Abstract: Small RNAs, especially microRNAs (miRNAs), play an essential role in the responses and adaptations of plants to many stresses, including salt stress. Characterizing miRNAs that correlate with salt stress will improve our understanding of salt tolerance and thus contribute to the sustainable production of maize. In our previous research, small RNA sequencing and degradome sequencing was performed on a maize inbred line (LH196), and many salt stress-responsive miRNAs and their targets were identified. In this study, the identity of target genes of miR164a was confirmed by quantitative expression analysis. Furthermore, the interactions between miR164a and its target genes were examined in a preliminary experiment using overexpression and target mimicry under salt treatment in maize. The results show that Zma-miR164 may respond to salt stress; because the expression of zma-miR164 was decreased with salt stress, leading to a significant increase in the expression of its target genes GRMZM2G114850 (the NAC transcription factor family proteins NAM, ATAF, and CUC) and GRMZM2G008819 (electron carrier). The NAC transcription factors respond to salt stress by regulating the expression pattern of their downstream genes.

Chloroplast DNA Variation Shed Light on the History of Lime Tree ( Tilia cordata s. l.) in the Eastern Part of the Range

Abstract: The Quaternary history of European nemoral forests in the east of their distribution may differ significantly from the typical dynamics of populations and ranges of most deciduous species in Western and Central Europe, characterized by survival in the Mediterranean refugia in glacial phases and recolonization in the interglacials. This study focuses on the phylogeography of the small-leaved lime Tilia cordata Mill. s. s. (Malvaceae) and related taxa in Eastern Europe, the Urals, Siberia, and the Crimea. The variability of five chloroplast DNA fragments (CDt, HKt, DT, K1K2, and psbJ–petA) was studied in 29 populations using restriction analysis and sequencing. The deep divergence of the six identified haplotypes and poorly supported topology of the phylogenetic tree presumably correspond to the long existence of T. cordata in several areas of the western Palaearctic isolated from each other. The two haplotypes dominate on the Russian Plain, in the Urals, and in Siberia. Their comparison with the data of other authors shows their absence in Western and Central Europe. Several haplotypes found in western Russia, in Belarus, and in Western Ukraine correspond to haplotypes previously identified in Central Europe and the Carpathians. We assume that such a distribution of chloroplast DNA variability is due to the preservation of lime in the refugia in the east of the range during one or several of the last glacial intervals and recolonization in the Late Glacial on the Russian Plain. Comparison of the results of the study of the variability of chloroplast DNA in T. cordata s. l. and the results of the study of nuclear microsatellites suggest that the species that lived in the Urals and the Russian Plain in the Pleistocene is a Siberian lime (T. sibirica), later displaced by the European small-leaved lime and now occurring only in Southern Siberia.

The Role of Satellite DNA in Causing Structural Rearrangements in Human Karyotype

Abstract: Satellite DNA, whose monomers form long arrays of tandem repeat ranging from hundreds or thousands of copies to several million base pairs, makes up at least 10% of the human genome. Application of new methods of sequencing and bioinformatics analysis opens the way to investigate the organization and functioning of human satellite DNA and contributes to the revision of the long-standing view about this part of the genome as “junk DNA.” One of the important features of satellite DNA is its participation in structural rearrangements in the human karyotype. This review examines the mechanisms of participation of satellite DNA in the formation of structural rearrangements, as well as the nature of transcription of tandem repeats in structural rearrangements in the karyotype of normal and tumor cells.

Genetic Mechanisms of Cognitive Development

Abstract: The results of large-scale meta-analyses of GWAS and genetic association studies demonstrated the role of allelic variants of a large number of genes in the development of cognitive abilities. Many of the identified genes are expressed in the brain and are involved in the pathogenesis of nervous system diseases. It has been shown that the summarized genetic effect for various cognitive abilities is no more than 50%. For certain genes, such as BDNF, DRD2, FNBP1L, PDE1C, PDE4B, and PDE4D, related to the regulation of neurogenesis and synaptic plasticity, associations with specific cognitive abilities were revealed. We assume the prospect of using the obtained results for the targeted effect in order to improve human cognitive abilities. This review describes DNA methylation, histone acetylation, expression of specific noncoding RNAs during brain functioning, and the development of individual differences in cognitive abilities. The revealed epigenetic mechanisms suggest the methods of reversible correction of cognitive functioning both in nonclinical forms and pathological states.

Gene Pool of Khakass and Shors for Y Chromosome Markers: Common Components and Tribal Genetic Structure

Abstract: The genetic structure of Khakass and Shor populations and clans (seoks) in terms of Y chromosome markers was investigated. The results of the analysis of haplogroup frequencies and YSTR haplotypes indicate that the Khakass and Shor seoks are related associations, in most cases having the same ancestor in the patrilineage. The gene pool of Khakass and Shors, more precisely a part marked by Y chromosome haplogroups, was shown to be primarily structured according to the generic principle. A strong genetic affinity of the members of the same seok was shown for the vast majority of the samples. Various Y chromosome haplogroups in the Khakass and Shor gene pools demonstrate their genetic affinity with Tuvans, Kets, Altaians, and Teleuts. This suggests the unity of the generalized gene pool of the indigenous South Siberian population and the genetic continuity of the populations living in this territory. Significant differences between the subethnic groups that are part of modern Khakass and Shors were revealed, where both of these ethnic groups were formed on the basis of common genetic components and demonstrate genetic affinity in various clans.

Morphological Genetic Markers in Plants

Abstract: The review discusses the possible use of morphological genetic markers in plants. Definitions and terminology of such concepts as “marker,” “phenotype,” “genotype,” “epigenotype,” and “genetic marker” are given. The properties and distinguishing features of genetic markers are given. Some mutant marker forms are described and the feasibility of creating and utilizing collections of mutant marker forms for their practical use in genetics and breeding of agricultural plants is considered. It is indicated that the main sources of genotypic variation, the basis, reflection, and manifestation of which is polymorphism, including marker polymorphism, which manifests itself not only at the morphological but also at the biochemical or molecular levels, are mutations and recombinations. The role and significance of the first phenotypic genetic markers obtained from the fruit fly Drosophila by means of experimental mutagenesis methods is noted; it allowed T. Morgan and colleagues to establish the exact location of the genes in the linkage groups and use it as a basis to create the first genetic “maps” of Drosophila chromosomes. The main disadvantages of morphological genetic markers are that they are few in number and are influenced by environmental factors or depend on the stage of development of the plant or its organ or tissue in which they are found. In addition, they do not cover the entire genome, but are located in certain genomic loci, in which the genes are concentrated. This means that it is not possible to use morphological markers that do not cover the entire genome for the purpose of genotyping or establishing genetic distances. However, despite these exceptions, morphological markers still remain a relevant and very useful scientific tool in genetic and breeding practices. Many of these markers are genetically linked to important economically significant and agronomic traits, which makes it possible to drastically reduce the cost and simplify the production of new forms significant for genetics and breeding. It is noted that the problem of genetic analysis of economically valuable traits can be a field of activity for further methodological optimization and “bridge building” between classical and molecular genetics and plant selection, as well as other biological disciplines.

MicroRNAs Associated with Preeclampsia

Abstract: MicroRNAs (miRNAs) are a class of small noncoding RNAs that play an important role in the mRNA regulation translation and degradation. Recent studies uncovered the implication of miRNA in the development of preeclampsia (PE)—a common and potentially fatal complication in pregnancy. This review provides an analysis of the current knowledge on miRNA associated with PE. We discuss the potential for using miRNA for the early diagnosis and prevention of PE. We briefly describe the miRNA targets associated with PE and point out the most promising PE predictors.

Molecular Phylogenetic Analysis of the Endemic Far Eastern Closely Related Oxytropis Species of Section Orobia (Fabaceae)

Abstract: The questions about the taxonomic status and phylogenetic relationships of the Far Eastern closely related species Oxytropis ochotensis, O. litoralis, O. erecta, O. ruthenica, and O. kunashiriensis of the section Orobia of the genus Oxytropis still remain unresolved. The study of the polymorphism of nucleotide sequences of the psbA–trnH, trnL–trnF, and trnS–trnG cpDNA intergenic spacers showed that populations of O. ochotensis and O. erecta are characterized by a low (0.378–0.495) haplotype (h) and a low (0.0006–0.0009) nucleotide (π) diversity, and in populations of O. ruthenica, h varies from 0.154 to 0.872 and π varies from 0.0002 to 0.0016. One O. ochotensis population from Magadan oblast and one O. ruthenica population from Russky Island (Primorsky krai) are monomorphic. Low nucleotide divergence of cpDNA between species O. ochotensis, O. erecta, and O. litoralis and also statistically insignificant genetic differentiation between them, the formation of a single haplogroup in the phylogenetic network, and the absence of species-specific molecular markers indicate the unity of their gene pool. A study of the ITS rDNA polymorphism revealed private ribotypes in O. ruthenica and O. kunashiriensis, the presence of a common ribotype in O. ochotensis, O. erecta, and O. litoralis, and the intraspecific polymorphism in O. ochotensis and O. erecta. The differences revealed in the chloroplast and nuclear genomes confirm the independence of O. ruthenica and O. kunashiriensis and suggest that O. erecta and O. litoralis are local phenotypes of the widespread polyploid species O. ochotensis. An analysis of the phylogenetic relationships of the cpDNA haplotypes showed a clear separation of O. ruthenica populations into two evolutionary lineages, but with a single ITS ribotype.

The Role of Mitochondrial DNA Individuality in the Pathogenesis of Parkinson’s Disease

Abstract: The present article reviews the rapidly growing body of research on the role of mitochondrial DNA (mtDNA) in the realization of individual risk of Parkinson’s disease. In this context, inherited mtDNA mutations, variants of its de novo polymorphism, haplogroup polymorphism, and accumulation of the mitochondrial genome somatic mutations are considered separately. Analysis of the reviewed published data shows that, at the moment, the haplogroup features and the mtDNA copy number should be considered the most proven risk factors for Parkinson’s disease. Data on similar importance of the mtDNA somatic mutations, its hereditary variants, and de novo mutations remain controversial and require careful study, primarily in animal and cell models.

The Emergence of Complex Dynamics during the Evolution of a Structured Limited Population

Abstract: The paper considers a microevolution model of two-stage population with limitation under the influence of natural selection that regulates juvenile survival rate. An analytical and numerical study of the model is performed; the parametric areas of various dynamic modes are determined. It is shown that an emergence of new alleles (for example, as a result of mutations) providing a greater reproductive potential of individuals leads to a natural selection of these alleles and evolutionary growth of the average value of the reproductive potential in the population. However, in the case of density dependent regulation of birth rate, the increase in the average value of reproductive potential leads to destabilization of the dynamics for the age group sizes. Scenarios of changes in the dynamics are various and depend on the parameter values of the model, but the main result is always the same: the dynamics become more and more complex and, as a rule, chaotic.

Cytogenetic Effects of Carbendazim on Mouse Bone Marrow Cells

Abstract: A study of the genotoxic activity of fungicide carbendazim was carried out. It was demonstrated that the tested technical grade active ingredient of carbendazim in the dose range of 125–2000 mg/kg body weight induced a statistically significant dose-dependent increase in the frequency of micronucleated polychromatic (PCE) and normochromatic erythrocytes (NCE) in the bone marrow of CD-1 mice. After administration of carbendazim at doses of 250–2000 mg/kg body weight, the accumulation of cells containing two or more micronuclei was observed. According to the results of comet assay, there was no increase in the level of breaks and alkali-labile sites in the DNA of the mouse bone marrow and liver cells after administration of technical grade carbendazim at doses up to 2000 mg/kg body weight. It is therefore suggested that the observed accumulation of cells with micronuclei is due to the aneugenic effect of carbendazim. In addition, a dose-dependent increase in the proportion of macrocytes/gigantocytes and dumbbell-shaped cells with constrictions among PCEs and NCEs was observed, which might be indicative of the inhibitory effect of the test pesticide on cytokinesis. The accumulation of polychromatophiles with pyknotic nuclei after exposure to carbendazim is probably caused by the distortion of nuclear extrusion. A possible general mechanism underlying the impairment of karyokinesis, cytokinesis, and nuclear extrusion in mammalian bone marrow erythroid cells is discussed.

Expression Features of the Transcription Factor Gene anthocyanin2 and Its Effect on the Anthocyanin Content in Capsicum chinense Jacq. Cultivars with Different Fruit Coloration

Abstract: The homologous anthocyanin2 (AN2) genes were identified and structurally characterized in two cultivars of hot pepper Capsicum chinense with different fruit exocarp coloration (purple and yellow). In the analyzed cultivars, the anthocyanin content and the expression pattern of the CcAN2 gene and anthocyanin pathway structural genes DFR and UFGT, regulated by AN2, were determined in the vegetative and reproductive organs, including fruit tissues at different stages of its development. A positive correlation between transcription levels of CcAN2, CcDFR, and CcUFGT was shown. A direct link between transcription levels of the analyzed genes and the anthocyanin content was observed in fruit peel, but not in the leaves. It was assumed that, in the vegetative tissues of the studied cultivars, the AN2, DFR, and UFGT genes can participate in plant photoprotection, and the visible purple color due to the anthocyanin accumulation may be associated with the regulatory activity of other MBW genes.

NRF2 and HMOX1 Gene Expression against the Background of Systemic Oxidative Stress in Patients with Acute Psychosis

Abstract: The aim of this study was to evaluate NRF2 and HMOX1 gene expression against the background of systemic oxidative stress in patients with acute psychosis. The study included 40 patients with newly developed paranoid schizophrenia, 22 subjects with new-onset acute psychosis associated with excessive alcohol consumption, and 25 healthy volunteers. The signs of systemic oxidative stress were assessed by 8-dihydro-2'-deoxyguanosine (8-oxodG) contents in peripheral blood lymphocytes (PBL) and in cell-free (cf) DNA samples obtained from plasma specimens of the patients and healthy controls. The patients of both groups demonstrated a significant (a hundredfold) increase in 8-oxodG content in cfDNA samples and a marked (5- to 8-fold) elevation of 8-oxodG concentration in PBL. Against the background of systemic oxidative stress, there was a statistically significant increase in NRF2 protein expression as well as marked elevation of NRF2 and Hmox1 gene transcriptional activity in PBL obtained from alcoholic patients. In contrast, the subjects with newly developed paranoid schizophrenia demonstrated decrease in expression of NRF2, the master regulator of anti-oxidant defenses, as well as reduction of NRF-2 and Hmox1 gene transcriptional activity compared to both healthy controls and alcoholic patients. In conclusion, against the background of systemic oxidative stress associated acute psychosis development, PBL of patients with paranoid schizophrenia was characterized by reduced NRF2 gene transcriptional activity and decreased NRF2 protein expression.

Genetic Differentiation of the Wolf Canis lupus L. Populations from Siberia at Microsatellite Loci

Abstract: A total of 270 gray wolf Canis lupus L. specimens from different regions of Siberia (Altai krai, Altai Republic, Republic of Tuva, Krasnoyarsk krai, Republic of Buryatia, Transbaikalia, and Yakutia) were studied at seven microsatellite loci. A high level of expected heterozygosity was observed (HE = 0.676), while there were no statistically significant differences in the indices of intrapopulation allelic and gene diversity between the samples. Low pairwise FST values (0.012–0.084; mean, 0.036) indicate that Siberian wolf populations are connected by active gene flow. Multivariate analysis of the genetic distance matrix (PCoA) showed grouping of samples in accordance with their geographical origin (Western, Middle, and Eastern Siberia). Clustering of multilocus haplotypes in the STRUCTURE v. 2.3.4 software program also demonstrated the presence of spatial subdivision, i.e., change in the contribution of different genetic clusters (K = 4) to the gene pool of the studied wolf samples from west to east and from south to north. In light of the genetic data obtained, the issue of the recognition and distribution of wolf subspecies is discussed.

Phylogenetic Relationships of Oxytropis Section Arctobia of Northeast Asia according to Sequencing of the Intergenic Spacers of Chloroplast and ITS of Nuclear Genomes

Abstract: Three intergenic spacers (psbA–trnH, trnL–trnF, trnS–trnG) of chloroplast DNA (cpDNA) and an internal transcribed spacer of nuclear ribosomal DNA (ITS rDNA) were used to study the genetic diversity and phylogenetic relationships of the species Oxytropis czukotica, O. exserta, O. gorodkovii, O. kamtschatica, O. mertensiana, O. nigrescens, O. pumilio, O. revoluta, and O. susumanica of the section Arctobia of the genus Oxytropis. According to cpDNA data, most populations are characterized by a low and medium haplotype (h varies from 0.154 to 0.583) and low nucleotide (π varies from 0.0002 to 0.0050) diversity. An analysis of the genealogical relationships of chlorotypes showed a clear separation of the studied taxa and the genetic proximity of O. nigrescens to O. susumanica and O. kamtschatica to O. exserta, the last two being the most diverged from all the others. In O. czukotica, three ITS rDNA ribotypes were detected; in O. nigrescens and O. susumanica, one common ribotype was found; and in all the others, one individual ribotype was identified for each species. According to the data of nucleotide polymorphism of markers of two genomes, the status of O. czukotica, O. gorodkovii, and O. pumilio taxa as a three separate species was confirmed. We suggest that O. susumanica is an intraspecific taxon of O. nigrescens. The revealed genetic similarities and differences of O. revoluta, O. exserta, and O. kamtschatica and their phylogenetic relationships do not correspond to the division of the Arctobia section into subsections; therefore, additional comprehensive studies are needed.

Genomic Selection. I: Latest Trends and Possible Ways of Development

Abstract: There is a forecast that global demand for foods of animal and plant origin will increase by 74% by 2050 (Food and Agriculture Organization of the United Nations). Satisfying this demand without a destructive effect on the environment is only possible while maintaining the principles of organic farming, as well as introducing new technologies in animal husbandry and crop production. Genomic selection as one of the most promising and safest methods for improving the genetic qualities of farm animals and plants can play a key role in this process. This review summarizes information on genomic selection, indicates possible growth points of this direction, demonstrates how a genomic estimation of the breeding value is constructed and what are the key conditions required for its implementation, and discusses the advantages and limitations of genomic and marker selection.

CYP2C9, CYP4F2, VKORC1 Gene Polymorphism in Buryat Population

Abstract: The allele and genotype frequency distribution at polymorphic loci rs1799853 (430C>T) and rs1057910 (A1075C) of the CYP2C9 gene, rs2108622 (1347C>T) of the CYP4F2 gene, and rs9923231 (1639G>A) of the VKORC1 gene in the Buryat population was examined. The study involved 197 volunteers living in the Republic of Buryatia: 124 woman and 73 men, average age of 57.51 ± 10.88 years. Genetic typing of DNA samples was performed by polymerase chain reaction (RT-PCR). The frequency of the minor alleles *2 and *3 of the CYP2C9 gene was 2.03 and 3.05%, respectively. The frequency of the allele T of the CYP4F2 gene was 31.22%; the frequency of the allele A of the VKORC1 gene was 85.28%. The obtained results could be used in the prognosis of pharmacotherapy of warfarin in the population Buryat population.

The Role of Oxytocin Receptor ( OXTR ) Gene Polymorphisms in the Development of Aggressive Behavior in Healthy Individuals

Abstract: Oxytocin represents one of the key element regulating social activity and aggressive behavior via its binding to oxytocin receptor (OXTR). Considering the multifactorial nature of developing aggression, the present study aimed to assess the main effects of the OXTR (rs53576, rs237911, rs7632287, rs2254298, rs2228485, rs13316193) gene polymorphisms together with haplotypic and G × E effects on individual differences in aggression level in 623 mentally healthy individuals with sex and ethnicity as covariates. The association of rs2228485*G allele (PFDR = 0.046) and rs237911*G allele (PFDR = 0.046) and decreased aggression level was observed in Tatars. Haplotypic analysis revealed an association of the OXTR G*G*G haplotype (rs53576, rs2228485, and rs237911) and diminished aggression level (Pperm = 0.020) in Tatars. As a result of multiple regression analysis, we observed the modulating effect of smoking and paternal overprotection significantly affecting association of the OXTR rs2228485 and aggression level (P = 0.029 and P = 0.014, respectively) in the total sample.

Vavilov’s Series of the “Green Revolution” Genes

Abstract: One hundred years ago N.I. Vavilov formulated the Law of homologous series in hereditary variability. Among the broad range of examples that encouraged N.I. Vavilov to make this important generalization, homologous series in plant height variability were mentioned. In the current review, we compare data collected over the century on genetic basis and molecular mechanisms behind the series in plant height variability with the stress on “Green revolution” genes. Application of fertilizers boosted redirection of artificial selection from tall-growing varieties to those with reduced height. The sources of GA-sensitive and GA-insensitive reduced height (Rht) genes in wheat and rice first were involved in crosses in Japan and China. The commercially valuable alleles of the Rht genes were spread broadly in varieties released in 1960s all over the world. Results of genetic studies into inheritance of the Rht genes are summarized for rice and wheat (together with further Triticeae crops–barley and rye). Three orthologous series of reduced plant height genes have been found within Triticeae tribe species and rice: (1) wheat Rht12 and rye Ddw1; (2) wheat Rht-B1/D1 and barley Dwf2; (3) barley denso/sdw1 and rice sd1. Molecular and cell mechanisms underlying plant reduced height are considered with focus on metabolic pathways regulated by commercially valuable alleles of Rht genes: GA-insensitive Rht-B1/D1 and GA-sensitive sd1, denso/sdw1, Rht8, Rht12, Rht18, Ddw1. Overall, in spite of similar metabolic pathways, the certain genes conferring variability for plant height are often distinct, resulting in existence of several “short” orthologous series of genes rather than one series through different cereal taxa.

The Inverse Comorbidity between Oncological Diseases and Huntington’s Disease: Review of Epidemiological and Biological Evidence

Abstract: The simultaneous development of several diseases (comorbidity, syntropy) in particular patients is a common phenomenon in modern clinical practice. However, the results of recent epidemiological studies have pointed to the new phenomenon of inverse comorbidity (or dystropy)—that means that some diseases can occur together in one person more rarely than in other people according to frequencies of these disorders in the population as a whole. Such dystropic (inversely comorbid) diseases are Huntington’s disease and oncological ones. In this paper, we perform a review of existing information supporting the hypothesis of the oncoprotection in carriers of HTT mutation, also including features of interactions of genes and proteins in such processes as autophagy and apoptosis.

Stress-Associated Cognitive Functioning Is Controlled by Variations in Synaptic Plasticity Genes

Abstract: The difficulties frequently caused by increased stress sensitivity while performing mathematical operations (mathematical anxiety, MA) represent an important problem for individual success. To date, no molecular-genetic studies have been published with respect to variations in math anxiety. According to “generalist genes hypothesis,” the genes involved in regulation of cognitive functioning and stress-associated component, including SNAP25, ARC, and GRIK1 genes, might be of interest to unravel the genetic nature of MA. Considering the necessity to include stress-related environmental factors in the analysis, the present study estimated both the main effect of SNAP25 (rs1051312, rs363050), ARC (rs2234911), and GRIK1 (rs2832407) gene polymorphisms and G × E interactions in individual differences in MA in 523 healthy individuals without cognitive decline with consideration of sex- and ethnicity-related differences. The association of SNAP25 rs363050*G allele with higher MA was observed in Tatars (P = 0.014, PFDR = 0.041, r2 = 0.044). As a result of multiple regression analysis, the G × E model including ARC (rs2234911)* order of birth affecting MA level was established (βST = 0.17, r2 = 0.017, Р = 0.049). The data obtained indicate the involvement of the SNAP25 and ARC genes

The Effect of Different Dominant VRN Alleles and Their Combinations on the Duration of Developmental Phases and Productivity in Common Wheat Lines

Abstract: Using allele-specific primers and hybridological analysis, the allelic composition of the VRN and PPD loci was determined in common wheat lines derived from the Bezostaya 1 (Bez1) cultivar. In lines of the Bez1 cultivar carrying different dominant alleles of the VRN genes and their combinations, the duration of certain developmental phases was examined. It was demonstrated that, in lines with the combination of two dominant alleles of the VRN-1 locus (Bez1Vrn-A1aVrn-B1a and Bez1Vrn-A1aVrn-B1c), the duration of the “tillering–first node” and “shoots–heading” periods was statistically significantly decreased compared to the initial isogenic lines (i:Bez1Vrn-A1a, i:Bez1Vrn-B1a, and i:Bez1Vrn-B1c). In addition, the presence of two dominant alleles led to the reduction in the time span of the organogenesis stages, as shown by studying the dynamics of shoot apex size and morphology in common wheat lines of the Bez1 cultivar. The productivity analysis in the lines of the Bez1 cultivar showed that the i:Bez1Vrn-B1c line was characterized by highest productivity among isogenic lines, while the Bez1Vrn-A1a Vrn-B1c line was more productive than the Bez1Vrn-A1a Vrn-B1a line.

Development of Molecular Markers Based on the L1 Retrotransposon Insertion Polymorphisms in Pigs (Sus scrofa) and Their Association with Economic Traits

Abstract: Molecular markers based on retrotransposon insertion polymorphisms (RTIPs) have great potential in studies of animal genetics and breeding. In this study, L1 RTIP markers were developed and evaluated by using microsatellite primers combined with L1 specific primers, and were further evaluated in four Chinese and three imported domestic pig breeds. Eight L1RTIP markers were obtained, and uneven distribution was observed among these breeds, with the Sujiang breed exhibiting the highest level of polymorphism with seven polymorphic sites, followed by Jiangquhai, Meishan, and Duroc with six, four, and four polymorphic sites, respectively. Both Landrace and Yorkshire pigs exhibited three polymorphic sites, while Chinese inbred Bama pig showed the lowest level of polymorphism with only one polymorphic site. Three polymorphic makers (L1-31-2, L1-31-5, and L1-31-11) were strongly associated with the economic traits in 462 Yorkshire pigs, with the L1-31-5+ genotype females had a significantly greater alive litter size (11.44 ± 2.80) compared with pigs with the L1-31-5– genotype (9.96 ± 2.89) (P < 0.05). L1-31-11– genotype pigs had significantly younger age at 100 kg of body weight (160.20 ± 10.26 days) than the L1-31-11+counter parts (162.47 ± 9.71 days) (P < 0.05). In summary, we demonstrated that it is feasible to develop markers based on L1 RTIP sin the pig, and these markers may have greater potential in the application of pig genetics and breeding compared to non-selective conventional breeding.

The Ability of Taxonomic Identification of Bifidobacteria Based on the Variable Regions of 16S rRNA Gene

Abstract: Bifidobacteria are considered key commensals of the human intestinal tract; they dominate the community in the earliest stages of life and are the first to respond to stress factors. The metasequencing of the V3–V4 16S rRNA fragments made it possible to identify 12 phylotypes of bifidobacteria in the gut microbiome of adolescents, which accounted for from 0.0001 to 0.9% of the total microbiome. A phylogenetic analysis of the obtained phylotypes was conducted; such species as B. angulatum, B. bifidum, B. longum, and B. animalis, as well as subspecies B. animalis subsp. lactis, were identified. The species of bifidobacteria excluded from identification by the V3–V4 variable regions were identified. The phylogenetic analysis of different variable regions and their combinations showed that a tree topology based on the V2 fragment is the most similar to a tree topology based on the complete gene.

Differences in the Amylase Inhibitor Gene SbAI Expression in Potato during Long-Term Tuber Cold Storage and in Response to Short-Term Cold Stress

Abstract: Expression analysis of the amylase inhibitor gene SbAI in five potato cultivars (S. tuberosum) revealed SbAI downregulation in tubers during long-term (seven months) cold storage. Estimation of SbAI gene expression and starch content in leaves of S. tuberosum cv. Nadezhda and four wild potato species (Solanum sect. Petota) showed a dramatic increase in SbAI transcription accompanied by starch content drop in response to short-term cold stress.

Genetic Evaluation of the Breeds of Reindeer (Rangifer tarandus) and Their Wild Ancestor Using a New Panel of STR Markers

Abstract: To study the genetic differentiation and phylogeny of the breeds and populations of reindeer (Rangifer tarandus L.), a test system based on multiplex PCR analysis of 16 highly polymorphic STR markers (Rt6, BMS1788, Rt30, Rt1, Rt9, FCB193, Rt7, BMS745, С143, Rt24, OheQ, С217, С32, NVHRT16, T40 and C276) was developed. Using this test system, 397 animals from 11 samples were studied. Four of these samples belonged to the wild forms of reindeer, while the rest of the samples represented the Nenets, Even, and Evenk breeds reared in different climatic zones of the Russian Federation. For 16 microsatellite loci, 204 alleles were identified, some of which could be considered breed-specific. It was demonstrated that more than 70% of the unique allele pool was concentrated in wild populations of reindeer. Statistical analysis of microsatellite data showed that the developed test system was an effective tool for identifying domesticated and wild forms of reindeer, testing the breed assignment, and determining the migration flows of a species over the vast territory of its distribution.

Noncanonical Functions of the Human Ribosomal Repeat

Abstract: Ribosomal genes encode ribosomal RNA (rRNA), which is an integral part of ribosomes. The main function of ribosomal genes in the cell is the synthesis of rRNA. However, ribosomal genes can also perform other functions in the body. It was found that DNA of ribosomal genes (rDNA) is an active biomolecule, which can be attributed to the family of DAMPs (danger-associated molecular patterns). Three unusual characteristics of rDNA confer to it the properties of a DAMP molecule: (1) high content of unmethylated CpG motifs—ligands of DNA sensing TLR9; (2) low oxidation potential; and (3) resistance to fragmentation under the accumulation of single-strand breaks in rDNA chains. Owing to these properties, rDNA fragments are accumulated as a part of circulating extracellular DNA and stimulate the TLR9–MyD88–NF-kB signaling pathway in various cells of the body. Oxidized rDNA permeates into the cells, where it can stimulate other DNA sensors (AIM2, RIG1, STING). Extracellular oxidized rDNA reaches the structures of the nucleolus and affects the level of rRNA in the cell. The body defends itself against the excess of extracellular rDNA by producing antibodies to rDNA, which form much stronger complexes with rDNA than common antibodies to double-stranded DNA. It is reasonable to further study extracellular rDNA as a potential target in the treatment of autoimmune, oncological, and cardiovascular diseases.

The FTO Gene and Diseases: The Role of Genetic Polymorphism, Epigenetic Modifications, and Environmental Factors

Abstract: The review provides information on the function of the FTO gene (known as the fat mass and obesity-associated gene) and the encoded enzyme, on the functional role of single nucleotide polymorphisms (SNPs) in coding and noncoding gene regions and the range of their competences, and on association of the FTO polymorphisms with diseases and traits. Factors that have modifying effect on the contribution of polymorphisms to the risk of disease development and trait variability are discussed. The FTO gene encodes alpha-ketoglutarate-dependent dioxygenase, which has a wide range of competences (including demethylation of RNA and single-stranded DNA), which are important for the functioning of the body. Nonsynonymous substitutions in the FTO gene lead to the development of orphan autosomal recessive disease (OMIM 612938). In the FTO noncoding regions, a wide range of variants has been detected, including those of regulatory importance (eQTL, sQTL, etc.). The competence of these variants extends to both FTO and neighboring genes (IRX3, IRX5, RPGRIP1L). Intronic polymorphisms of the FTO gene have been found to be associated with a wide range of multifactorial diseases and traits (obesity and related anthropometric traits, lipid metabolism markers, diabetes mellitus (type 2), coronary heart disease, metabolic syndrome, and other diseases). In the overwhelming majority of studies, the same allele variants are classified as risk ones; however, previously established associations of the FTO polymorphisms with diseases (traits) are demonstrated not in all populations. It is demonstrated that the effects of the FTO gene SNPs can be modified by exogenous and endogenous environmental factors, as well as lifestyle (including the type of diet, consumption of certain nutrients and medications, physical activity, etc.). Epigenetic factors (DNA methylation at CpG sites) are also important for regulating the level of FTO expression and the effects of individual SNPs. The accumulated data on the FTO structure and function, as well as the functional role of the encoded enzyme, make this gene attractive from the point of view of developing personalized approaches to healthcare.

Specific Lux Biosensors of Escherichia coli Containing pRecA::lux, pColD::lux, and pDinI::lux Plasmids for Detection of Genotoxic Agents

Abstract: The lux biosensor of E. coli MG1655 (pDinI::lux) was constructed and a comparative study of the SOS response of three biosensors E. coli MG1655 (pRecA::lux), E. coli MG1655 (pColD::lux), and E. coli MG1655 (pDinI::lux) under the action of genotoxic agents was performed. The listed biosensors were named, respectively, PRecA, PColD, and PDinI. The response amplitude (RA) was chosen as an indicator of the SOS response level of lux biosensors. It was shown that RA of the PDinI biosensor was more expressed than RA of the PRecA biosensor under the action of hydrogen peroxide, alkylating agents such as NMU, MMS, and streptozotocin, antibacterial agent such as dioxidine, and cytostatics such as mitomycin C and cisplatin. Antimetabolite 5-fluorouracil showed activity only with PDinI. Furacilin and 4-NQO, whose metabolites form adducts with DNA, were more active on PColD than on PRecA and PDinI. DNA gyrase inhibitors such as nalidixic acid and ciprofloxacin were less active on PDinI than on PColD and PRecA. Overall, among 13 tested substances, 8 more actively induced SOS response in the PDinI biosensor than in PColD and PRecA. At the same time, 5-fluororacil induced SOS response only with the PDinI biosensor. It was concluded that the PDinI biosensor can be successfully used for the primary detection of potential genotoxicants by their ability to induce SOS response in E. coli cells.

Morphological and Genetic Variability of Sympatric Whitefishes of the Coregonus lavaretus pidschian Complex from Lake Kutaramakan of the Khantaisk Drainage System (Taymyr Peninsula)

Abstract: This work presents the results of morphological and genetic analyses of the sympatric forms/species of whitefishes of the Coregonus lavaretus pidschian (Coregonus pidschian) complex from Lake Kutaramakan of the Khantaisk drainage system (Taymyr Peninsula). It is found that the studied whitefish forms/species do not differ in the number of gill rakers on the first branchial arch, but are well distinguished by the number of perforated lateral line scales, most morphometric characters, and biological features. Analysis of variability of the mitochondrial ND1 gene shows that whitefishes from Lake Kutaramakan belong to two different phylogenetic lineages which were earlier found in water bodies of the Taymyr Peninsula, the Ob, Yenisei, and Anabar rivers. It is shown that some whitefish haplotypes belong to pidschian-like whitefish from the Ob River basin and other haplotypes belong to glacial-plain whitefish C. lavaretus pidschian natio glacialis (C. lavaretus pidschianglacialis). Unlike whitefishes from the Anabar River, where such forms are strongly differentiated, there is considerable hybridization between the forms in Lake Kutaramakan.