Vavilovskii Zhurnal Genetiki i Selektsii最新文献

Occupying a fairly extensive territory within the East European Plain, representatives of the Chernyakhov culture interacted with many synchronous tribes of other cultures inhabiting neighbouring regions. The question of a possible Proto-Slavic component in the population of the Chernyakhov culture is a subject of many years of discussion, but there is still no evidence for the genetic contribution of representatives of this culture to the gene pool of the Slavs in the subsequent historical period. In this study, we present the results of the craniological and genetic analysis of an individual from the Krynichki burial ground, presumably belonging to the Slavic part of the population of the Chernyakhov culture. A craniometric comparative analysis was conducted for several series of skulls of the East Slavs and representatives of the Chernyakhov culture. The comparison of intragroup variability in the groups of the two cultures showed marked differences between them in the first three principal components. At the same time, the East Slavic and Chernyakhov cultures have similar levels of craniological variability. Differences between female specimens are not so pronounced as those of males'. Based on the analysis of whole-genome sequencing data, the individual from the Krynichki was identified as being a female. The complete sequence of mitochondrial DNA, which belongs to the haplogroup H5a1a1, was reconstructed. For this mitochondrial lineage, a phylogenetic relationship was revealed with eight specimens from publicly available genomic databases, five of which belong to representatives of the present-day West and East Slavic populations. Furthermore, we revealed a mitochondrial sequence identical to that from our previous research on an individual from a medieval burial site located in the modern Vologda region, which is thought to have Slavic ancestry. The complete match between the medieval individual's mtDNA sequence and that of a representative of the Chernyakhov culture points to their likely maternal ancestry. Thus, a possible continuity between representatives of the Chernyakhov culture (3rd century AD) and the population of Ancient Rus' (the second half of the 12th-early 13th centuries AD) has for the first time been shown, as genomic data suggest.

Recalcitrance is defined as the inability of plant species or individual genotypes to effectively regenerate and/or to be transformed in in vitro culture, and is the most significant limitation for genome editing of agricultural crops. To develop protocols for genotype-independent transformation and regeneration of cultivated plants, knowledge of the genetic factors that determine recalcitrance in various plant species under in vitro conditions is required. Their search by classical QTL mapping in populations segregating for callus formation efficiency, regeneration, and transformation is considered a complex and labor-intensive process due to a specific nature of the analyzed phenotypes and a strong genotype-environment relationship. The article provides an overview of the methodology, prospects, and most outstanding achievements of "forward" genetics in identifying genetic determinants of recalcitrance in the most popular and at the same time most difficult to work with in vitro cereal and legume crops. Examples of genetic mapping and successful cloning of genes responsible for various aspects of recalcitrance in cereals are discussed. Thus, it was found that the formation of rapidly proliferating type II embryogenic callus in maize is determined by increased expression of the Wox2a gene. The Koshihikari rice variety, popular in Japan, poorly regenerates in vitro due to impaired nitrate metabolism, since it has a low expression level of nitrite reductase (NiR), which converts nitrite into ammonia. Callus browning, which occurs among many plant species and leads to a decrease in regenerative capacity and even to plant death, in rice varieties (Oryza sativa ssp. indica) depends on the expression level of the Browning of Callus1 (BOC1) gene, which encodes the SRO protein (Similar to RCD One), regulating the plant response to oxidative stress. Similar studies on mapping loci for somatic embryogenesis traits in soybean have revealed major QTLs explaining 45 and 26 % of phenotypic variation. Studies on genetic mapping of loci affecting the efficiency of regeneration and embryogenesis in recalcitrant plant species have obvious prospects due to the emergence of annotated reference genomes, high-throughput genotyping and high-resolution genetic maps.

The induced "recombinogenic situation" in hematopoietic stem cells and the activation of the cell's reparative systems create the basis for recombination events between fragments of extracellular double-stranded DNA delivered into the cell and chromosomal DNA or other forms of the reparative-recombination process. In mouse and rat model organisms as well as in human bone marrow cells, changes in the amount of telomeric DNA in hematopoietic stem cells were assessed as an indicator of repair and recombination events that have occurred. In all experiments performed, recombinant human angiogenin was used as a comparison factor. Dot blot hybridization showed that in the colony cells obtained from the bone marrow cells of the model organisms as well as from human bone marrow cells treated with a double-stranded DNA preparation, there was a significant increase in the amount of telomeric DNA. Amplification of telomeric DNA in colony cells is not associated with contamination of the original DNA preparation with which the bone marrow cells were treated. Treatment of bone marrow cells with DNA that does not carry telomeric sequences (AluI PCR fragment) does not lead to an increase in the amount of telomeric DNA in the cells of grown colonies. This suggests the participation in the amplification of telomeric DNA of an extrachromosomal DNA template carrying telomeric DNA. It has been established that treatment of bone marrow cells with angiogenin also leads to an increase in telomeric DNA in colony cells. A comparison of the type of colonies with the intensity of hybridization (i. e. the amount of telomeric DNA in the sample) suggests that the increase in the amount of detectable telomeric DNA following treatment with angiogenin and hDNAgr has a fundamentally different origin. Western blot analysis and real-time PCR revealed that the increase in the amount of telomeric DNA following treatment of bone marrow cells with a double-stranded DNA preparation does not correlate with the activity of endogenous/exogenous telomerase. For angiogenin, it has been shown that an increase in the amount of telomeric DNA may be the result of activation of endogenous telomerase activity. A principle has been developed for the amplification of a new genetic trait that came into hematopoietic stem cells with extracellular double-stranded DNA material and was fixed in the recipient genome or was transitively present in the cell as new genetic information.

One of the ways to increase yield stability of bread wheat under changing climatic conditions is through improving the photosynthesis efficiency. For this purpose, various genetic strategies are used. They include marker-assisted selection and the use of the genetic potential of wild wheat relatives. Previously, using introgression wheat lines carrying different segments of chromosome 2D from Aegilops tauschii in the genetic background of the wheat (Triticum aestivum) variety Chinese Spring (CS), we mapped QTLs associated with variability in shoot biomass and gas exchange under contrasting water supply conditions. In this work, by "splitting" the primary introgressions, we obtained secondary introgression CS lines with reduced segments of Ae. tauschii introgressions in the short and long arms of chromosomes 2D. The aim of this study was to investigate the tolerance of the photosynthetic apparatus to soil water deficit in these lines. We estimated the size of drought effect on shoot biomass, gas exchange parameters, photosynthetic pigment content, slow and fast chlorophyll fluorescence parameters, and fast light curve parameters. The results showed that line 1004 with an introgression in chromosome 2DS limited by microsatellite loci Xgwm296 and Xgwm261 was little affected by drought in respect of the chlorophyll (a+b)/carotenoid ratio and primary photosynthetic processes. In line 1005 with a single introgression in the region of the Xgwm261 marker, the chlorophyll (a+b)/carotenoid ratio and indicators of the functional activity of photosystems significantly decreased under water deficiency. The chlorophyll (a+b)/carotenoid ratio, CO2 assimilation rate, and chlorophyll fluorescence parameters remained stable in line 1034 with an introgression in chromosome 2DL near the Xgwm1419 and Xgwm157 loci. In line 1021 with an introgression in the region of the Xgwm539 marker on the same chromosome, we observed a strong negative effect of drought on the rate of CO2 assimilation and indicators of the functional activity of photosystems. The Xgwm1419 and Xgwm296 markers can be recommended for use in marker-assisted breeding for drought tolerance of bread wheat in the cases where Ae. tauschii acts as a donor of genetic material.

Pseudomonas aeruginosa is one of the leading causes of nosocomial respiratory tract infections and plays an important role in lower respiratory tract infection in patients with cystic fibrosis (CF). Biofilms, which are organized cell clusters, ensure the survival of microorganisms in unfavorable environmental conditions and contribute to the chronicity of infection and the formation of persistent forms. The aim of this study was to determine the phenotypic ability and genetic potential for biofilm formation in clinical strains of P. aeruginosa persisting in patients with CF against the background of constant intake of antimicrobial drugs. Bacteriological, genetic, and bioinformatic methods were used to characterize five P. aeruginosa strains obtained from patients with CF. Phenotypically, all strains were classified as moderately biofilm-forming, while the biofilm formation coefficient varied from 2.10 to 3.15. Analysis of draft genomes revealed differences in the representation of some genes or individual loci of three of the four known signaling pathways (cAMP/Vfr, Gac/Rsm, and c-di-GMP) that have been described in P. aeruginosa genomes and are related to the regulation of biofilm formation. In addition, differences in the representation of genes such as frzE, tcpE, and rcsC are shown. Of undoubted interest is the analysis of genes such as pppA, icmF, clpV1, trpE, trpG, and stp1, which are used for extended multilocus typing PubMLST and differed in the structure of loci in all analyzed strains. These genes can be used to identify clinical strains of P. aeruginosa and to characterize their biofilm-forming properties. Thus, genes potentially participating in both biofilm formation and regulation have been characterized in the genomes of clinical P. aeruginosa strains that persist for a long time in patients receiving continuous antibiotic therapy. Characterization of the genetic potential for biofilm formation makes it possible to search for reliable genetic markers of this process in order to monitor the evolution of the pathogen as a result of long-term persistence in the host organism.

The number of grains of a cereal plant characterizes its yield, while grain size and shape are closely related to its weight. To estimate the number of grains, their shape and size, digital image analysis is now generally used. The grains in such images may be completely separated, touching or densely packed. In the first case, the simplest binarization/segmentation algorithms, such as the watershed algorithm, can achieve high accuracy in segmentation and counting grains in an image. However, in the case of touching grains, simple machine vision algorithms may lead to inaccuracies in determining the contours of individual grains. Therefore, methods for accurately determining the contours of individual grains when they are in contact are relevant. One approach is based on the search for pixels of the grain contact area, in particular, by identification of concave points on the grain contour boundary. However, some grains may have chips, depressions and bulges, which leads to the identification of the corner points that do not correspond to the grain contact region. Additional data processing is required to avoid these errors. In this paper, we propose an algorithm for the identification of wheat grains in an image and determine their boundaries in the case when they are touching. The algorithm is based on using a modification of the concave point search algorithm and utilizes a method of assigning contour boundary pixels to a single grain based on approximation of grain contours by ellipses. We have shown that the proposed algorithm can identify grains in the image more accurately compared to the algorithm without such approximation and the watershed algorithm. However, the time cost for such an algorithm is significant and grows rapidly with increasing number of grains and contours including multiple grains.

The theory of Pleistocene refugia is often used to explain the population genetic structure of species. However, it does not fully account for the diversity of species-specific characteristics and natural conditions. The genus Pica, which is widespread in the Holarctic, provides an ideal model for studying phylogeographic patterns in order to better understand processes of diversification and speciation. Markers of mitochondrial DNA remain widely used in phylogeographic studies, despite advances of whole genome techniques. We have summarized published research on the mitochondrial DNA Control Region (CR) variation, based on data from 279 samples which represent the majority of extant taxa across the entire distribution range of the genus. In the phylogenetic trees and networks, we found several cases of reciprocal monophyly among most allopatric species and subspecies, and in addition some examples of paraphyly and polyphyly. Bayesian skyline plots were calculated to explore population dynamics over time. They showed varying longevity of the lineages since their origin or after experiencing a bottleneck, e. g., in the case of the Kamchatka population, as well as unequal rates of expansion. In most cases, speciation followed a geographic model involving expansion and vicariance, sometimes with divergence in refugia. Somewhere, peripatric speciation may have happened due to separation of a marginal populations. By comparing haplotype composition among populations, we traced the origin of the recently established populations on Hokkaido and Kyushu islands from a limited number of colonizers from the mainland. Isolated cases of species in statu nascendi were identified through evidence of incomplete lineage sorting, leading to paraphyly, or signs of limited unidirectional interspecies introgression of nuclear genes in secondary contact zones. Several hypotheses regarding the formation of the magpie´s range are proposed. Various evolutionary scenarios found in the genus Pica were compared to those reported for the other bird species in a number of literature sources.

Despite numerous efforts of the global community, it is still not possible to stop the HIV/AIDS pandemic. To stop the spread of the virus, an effective preventive vaccine is needed, as well as the search for new antiviral agents. In order to be able to quickly and adequately evaluate the developed vaccine constructs, characterize HIV-specific antibodies and potential drugs, a reliable testing method is needed. In this regard, pseudotype neutralization assays using a panel of Env-pseudoviruses of different HIV-1 subtypes has proven itself well. Currently, separate panels of Env-pseudoviruses of the main genetic subtypes of HIV-1 (A, B, C and a number CRFs) have been created. These panels are necessary to obtain standardized data sets that can be used to rank the effectiveness of the vaccine and identify promising candidates for further study. Currently, the HIV-1 subtype A6 dominates in the European part of Russia, and the recombinant form CRF63_02A6, which has currently been detected in more than 80 % of new HIV-1 cases in Siberia, dominates in Siberia. The aim of this work was to expand and characterize the collection of Env-pseudoviruses obtained on the basis of the recombinant form CRF63_02A6 of HIV-1 circulating in Siberia. In this study, two new variants of Env-pseudoviruses based on CRF63_02A6 of HIV-1 were obtained, characterized, and included in our collection. At present, the collection includes 13 Env-pseudoviruses that are CCR5-tropic. Phylogenetic analysis of the full-length nucleotide sequences of the env gene confirmed that all 13 pseudoviruses cluster with the reference sequences of the recombinant form CRF63_02A6. The Env-pseudoviruses were characterized using broadly neutralizing antibodies (bnAbs) targeting different regions of vulnerability of HIV-1 located on the surface of Env glycoprotein complexes. It was shown that the Env-pseudoviruses are sensitive to neutralization by bnAbs VRC01 and 10E8; moderately sensitive to neutralization by bnAbs PG9 and PGT126; and resistant to neutralization by antibodies 2G12 and 2F5. The resulting collection is an important addition to the existing panels of pseudoviruses against other HIV-1 subtypes in the world.

The genomes of Solanaceae plants contain over 600 receptor-like protein kinase genes with leucine-rich repeats (LRR-RLK), many likely associated with pathogen detection, but very few functionally characterized. Pectobacterium spp. are the major bacterial pathogens of agricultural crops, particularly potatoes and other Solanaceae plants. For relevant potato pathogens from the genus Pectobacterium, specific immune receptors have not been described in Solanaceae. However, in Malus × domestica, four LRR-RLK from the LRRIII subfamily (DIPM1-4) have been characterized as receptors for the related pathogen Erwinia amylovora. DIPMs specifically interact with the effector protein DspE and are involved in E. amylovora recognition. Since the DspE ortholog is also the main effector in Pectobacterium spp., we performed a phylogenetic analysis of LRRIII subfamily receptors in the most relevant Solanaceae representatives together with a much better characterized LRR-RLKIII of Arabidopsis thaliana and identified nine clusters of related RLKs. Clustering followed by analysis of published data allowed us to functionally characterize this RLK family and suggest the most likely candidates for checking interactions with the main effector of pectobacteria, DspE. Testing the kinase domains of representative cluster members in a yeast two-hybrid system revealed four Solanaceae RLKs interacting with the DspE effector from Pectobacterium versatile. Virus-induced silencing of these RLK genes demonstrated their involvement in P. versatile recognition. The RLK6 gene from Solanum bulbocastanum, which is not an ortholog of the DIPM proteins in apple, seems to be the most promising potential resistance gene. This work expands our understanding of LRR-RLKIII subfamily RLKs and their role in plant immunity, providing a foundation for future development of disease-resistant Solanaceae varieties.

Grafting with resistant rootstocks is one of the most effective methods to prevent soil-borne diseases, and it can influence vegetative growth, flowering, maturation periods, and fruit quality, thereby ensuring high yields. In this study, four species from the family Cucurbitaceae were tested as potential candidates for grafting cucumber and melon: Cucurbita ficifolia Bouché, Cucurbita moschata L., Cucurbita pepo L. and Cucurbita maxima Duch. The study focused on the grafting methods that optimize growth parameters and the accumulation of hormones and vitamins in rootstock. The results indicated that Cucurbita maxima Duch. is the most suitable rootstock material for grafting to Cucumis sativus L. and Cucumis melo L., as it exhibited superior plant and root mass. Among the two grafting methods tested, the tongue approach ('X') demonstrated the best results in terms of growth parameters and the accumulation of indole-3-acetic acid (IAA) and vitamins in the scion leaves. IAA and vitamin concentrations were measured using HPLC in grafted samples at 2, 4 and 6 weeks of age. In the 'X' method, IAA accumulation from the end of the second week was twice as high compared to control plants. This method also showed higher vitamin content, with increased levels of B vitamins and vitamin C at the end of the 4th week (25.2-135.1 and 52.3-67.0 %, respectively), and vitamins A, E, D3 , K starting from the 2nd week (1.5-2 times higher). Conversely, the insertion or slant cut grafting method ('Y') did not show any significant increase in the analyzed parameters and was comparable to the control. The 'X' method for grafting both Cucumis sativus L. and Cucumis melo L. onto Cucurbita maxima Duch. plants demonstrated the best results and is recommended for production.