Vavilovskii Zhurnal Genetiki i Selektsii最新文献

Approximately 10-15 % of clinically recognized pregnancies result in miscarriage, with chromosomal abnormalities identified in about 50 % of early pregnancy losses (PL). Triploidy accounts for approximately 12 % of all chromosomal abnormalities in miscarriages. The additional haploid set of chromosomes in triploidy may be of paternal (diandric triploidy) or maternal (digynic triploidy) origin. Diandric triploidy is associated with a partial hydatidiform mole (PHM), while pregnancies involving diploid embryos with two paternal genomes (and loss of the maternal nuclear genome) are the most common cause of a complete hydatidiform mole (CHM). The hydatidiform mole (HM) is the most prevalent form of gestational trophoblastic disease. Genotyping of products of conception (POC) is currently considered a reliable method for confirming HM and distinguishing its subtypes. The aim of this study was to use DNA genotyping of POCs to detect cases of triploidy, estimate the frequency of HM and its subtypes, and analyze the molecular and clinical characteristics of triploid pregnancies, CHM, and PHM in a Russian population. Between 2018 and 2024, a total of 10,000 consecutive PL cases were analyzed at the Medical Genetic Center Progen (Moscow). The main clinical indications included spontaneous miscarriage, missed miscarriage, and anembryonic pregnancy. DNA genotyping was performed using a five-color multiplex QF-PCR method, which included profiling of 26 autosomal STR markers, as well as DYS437, DXS6809, the SRY gene, and 30 markers from homologous regions located on different chromosomes. CHM was diagnosed based on the homozygosity of all STR markers. Triploidy was identified by analyzing peak area ratios of non-homozygous STR markers, which exhibited characteristic patterns of approximately 2:1 or 1:1:1. In our cohort, chromosomal abnormalities were identified in 58.8 % of all PL cases. Triploidy was detected in 8.3 % of the total sample, representing 14.3 % of all chromosomally abnormal POCs. Diandric triploidy accounted for 43 % of triploid cases. The prevalence of CHM was 0.11 %. The median age of women with triploidy was 32.1 years, and 27.9 years for those with CHM. Given the observed frequencies of PHM and CHM in our cohort, along with the relatively young maternal age associated with these conditions, enhancing current diagnostic protocols for HM - particularly through the incorporation of DNA genotyping of POCs - is essential for the effective prevention and timely diagnosis of post-molar malignant neoplasms in this population.

Uniparental disomy of chromosome 9, in combination with low-level mosaicism for chromosome 9, represents a rare chromosomal disorder. One of the mechanisms underlying the formation of uniparental disomy is the trisomy rescue, which concurrently results in low-level mosaicism. The diagnosis of mosaic aneuploidies poses significant challenges due to the limited sensitivity and resolution of conventional cytogenetic methods, which often fail to detect low-level mosaicism. Additionally, the variable distribution of cell lines within the patient's tissues, as well as the heterogeneity of samples derived from the same tissue, complicates the precise determination of the impact of mosaic trisomy on the phenotypic expression. Phenotypic manifestations associated with mosaic trisomy 9 are characterized by considerable variability. During the prenatal period, intrauterine growth restriction is frequently observed in cases of this chromosomal abnormality, although this finding is not pathognomonic for the condition. In liveborn infants with trisomy 9 mosaicism, characteristic phenotypic features may include craniofacial anomalies (such as micrognathia and ear malformations), scoliosis, low-set ears, feeding and respiratory difficulties, hip dysplasia, seizures, and developmental delays. To establish a diagnosis in a patient presenting with multiple dysembryogenic stigmata and psychomotor retardation, a comprehensive molecular cytogenetic analysis was conducted. This included high-resolution chromosomal microarray analysis (CMA) and fluorescence in situ hybridization (FISH) using targeted DNA probes. CMA identified regions of loss of heterozygosity (LOH) on chromosome 9, indicative of uniparental disomy, and suggested the presence of low-level mosaicism for trisomy 9. Subsequent FISH analysis of cultured lymphocytes, employing DNA probes specific to various regions of chromosome 9, confirmed the low-level mosaicism for trisomy 9. The results of our study are consistent with the idea that mosaicism for chromosome 9, particularly when combined with uniparental disomy, constitutes a complex genetic anomaly that can lead to a spectrum of phenotypic manifestations, including developmental delay, growth abnormalities, and behavioral anomalies. CMA and FISH are highly effective methods for the diagnosis of uniparental disomy and low-level mosaicism involving chromosome 9.

A paracentric inversion (PAI) is a rare type of balanced intrachromosomal structural rearrangement. Heterozygotes for PAI are usually phenotypically normal, but the presence of the inversion may occasionally lead to synapsis and recombination disruptions during meiosis. PAI can be responsible for the production of recombinant chromosomes and unbalanced gametes. The risks associated with the birth of a child with chromosomal imbalances due to the generation of unbalanced crossover gametes is considered to be low. Nonetheless, viable offspring with intellectual disabilities and/or congenital abnormalities, as well as early miscarriages, stillbirth and infertility in heterozygous carriers of PAI have been described. Paracentric inversions may arise on various chromosomes. PAI with breakpoints on the long arm of chromosome 7 is among the most prevalent ones in humans. To assess the meiotic behavior of abnormal chromosome 7, as well as the empirical risk of producing gametes with recombinant chromosomes, the sperm FISH analysis of a male heterozygous carrier of inv(7)(q11.23q22) was performed. The percentage of recombinant sperms was 0.7 % and chromosomal imbalance was represented as reciprocal breakage products of a dicentric chromosome 7. Notably, spermatozoa with a dicentric chromosome 7 were not observed, which confirms its instability during meiosis I. Meiotic segregation analysis in the heterozygous carrier of inv(7)(q11.23q22) revealed a predominant formation of gametes containing either the inverted or the intact chromosome 7, occurring at frequencies of 52.2 and 47.8 %, respectively. This report is the first study providing a detailed description of meiotic segregation patterns of inv(7)(q11.23q22) by using a sperm FISH approach. Recombinant gamete formation confirms the occurrence of crossing-over within the inversion loop. Consequently, the individual risk of generating gametes (and subsequent zygotes) with chromosome 7 imbalance for this heterozygous carrier remains low.

Data on mitochondrial DNA (mtDNA) polymorphism at the population level are of significant interest to researchers in the fields of population and ethnic genetics, forensic medicine, and forensic science. In the present study, we have obtained data on the variability of whole mitochondrial genomes in the immigrant East Slavic population of Northeastern Siberia (using the Magadan region as an example). The study yielded novel data concerning mtDNA variability in the Magadan region's inhabitants comprising maternal lineages of Russians (N = 49) and Ukrainians (N = 15), as well as individuals with a mixture of maternal and paternal ancestries, including Russians on the maternal side and indigenous populations (Koryaks, Evenes, and Itelmens) on the paternal side (N = 4). In addition, the mitogenomes of the Russian population from the Novgorod, Kaluga, and Yaroslavl regions (N = 15) were sequenced to enhance the power of the phylogeographic analysis. The results of the study demonstrated that the mitochondrial gene pool of the East Slavic immigrant population in the Magadan region is characterized by a high level of diversity. The analysis of genetic differentiation of Russian populations within Russia, as measured by the variability of complete mitochondrial genomes, revealed a low level of interpopulation differences (Fst = 0.15 %, P = 0.2). The results of multidimensional scaling of Fst distances indicate that the Russians residing in the Magadan region are genetically similar to the Russian populations inhabiting the southwestern part of the country, specifically the Belgorod and Orel regions. The gene pool of the Russian population in the Magadan region is predominantly characterized by mtDNA haplotypes of West Eurasian (including European) origin. The prevalence of East Asian-derived haplotypes among the Russian population is relatively low, accounting for approximately 4.8 % of the total. However, certain East Asian-specific haplogroups, such as F1b1 and Z1a1a, have demonstrated a prolonged presence in the gene pools of Eastern European populations, as evidenced by phylogeographic analysis. Among the European mtDNA haplotypes of Russians from the Magadan region, Eastern European variants predominate, and they also have a high proportion of mtDNA haplotypes specific to Slavs (19.4 %). Furthermore, rare mtDNA haplotypes have been identified in the mitochondrial gene pools of Russians and Ukrainians residing in the Magadan region. These rare haplotypes are linked to the maternal lines of Empress Alexandra Fedorovna Romanova (haplogroup H1af2) and Prince Dmitry, son of Prince Alexander Nevsky (haplogroup F1b1-a3a2a).

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.