Genetic Certification Research Articles

СРАВНИТЕЛЬНЫЙ АНАЛИЗ ВЫДЕЛЕНИЯ ДНК ИЗ УШНЫХ ТКАНЕЙ И ХВОСТОВ СВИНЕЙ (SUS SCROFA DOMESTICUS)

Extraction of DNA from tissue samples is the initial stage in molecular genetic studies of farm animals. Cur- rently, in the Russian Federation, the creation of extensive DNA biobanks for deep retrospective analysis for the purposes of genomic selection is relevant. In the livestock industry, studies of the genome and transcriptome of pigs (Sus scrofa domesticus) are especially important for identifying new genetic markers of economically valua- ble animal traits and developing effective postgenomic approaches to targeted selection, genetic certification and obtaining lines with new characteristics. The purpose of this study was to determine and compare the quality and quantity of DNA obtained from tissue samples of ear notches and tails of pigs using a commercially available kit by the method of sorption on magnetic particles «Tissue M», Raissol Bio (Russia). As a result, both types of bio- logical samples showed a high yield of DNA, however, the maximum DNA concentrations were observed when using tail samples (725.1 ng/μl) and, in general, the average result was higher (337.2 ng/μl) than when using ear notches (146 ng/μl). The spectral characteristics of the obtained DNA also showed a good result within the per- missible values. Quality control of the isolated DNA using PCR with a «random» primer showed its high quality and suitability of the obtained DNA for subsequent molecular genetic studies. Thus, based on the data obtained, it was concluded that piglet tails are suitable as biological material for isolating high-quality genomic DNA for fur- ther molecular genetic studies.

Analysis of the Genetic Structure of 29 Horse Breeds of Russian Selection by str Markers

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

Information support for the bioresource collection: a biological information system «NeuroOnc»

The manuscript is devoted to development of information support system for a bioresource collection - biological information system «NeuroOnc». Architecture and main functions of system are presented. This system was formed in the project «Development of bioresource collection of tumors of the human nervous system with molecular genetic certification for personalized treatment of patients with neuro-oncological diseases». The purpose of this project was not only formation of bioresource collection, but also development of various molecular genetic methods for analysis of biospecimens in context of clinical researches. Biological information systems created to support the work of bioresource collections in hospitals should become a natural part of information infrastructure. Information support of bioresource collections cannot imply only «warehouse» functions. This system should have tools to support various scientific and clinical researches. Biological information systems can sometimes expand medical information systems but remain sufficiently autonomous. It is advisable to develop biological information systems in large specialized companies that can support their products for many years.

Terminology Issues in the Field of Genetic Research

Due to the intensive development of genetic research, the availability of genetic testing is increasing, including those based on genome-wide sequencing offered by private and public laboratories. Genetic testing can be used to identify the cause of the disease in patients with suspected hereditary (orphan) diseases and as a screening tool for healthy people, for example, if expectant parents planning to have children are carriers of hereditary diseases, to identify the risks of hereditary oncological diseases and multifactorial diseases, for pharmacogenetic testing, as well as for non-medical purposes, for example to determine the «ethnic origin». In addition, genetic research can be used to identify individuals, including in criminology and for genomic registration, determination of paternity and other kinship. This review paper analyzes some issues of terminology in the field of genetic research, including their results, as well as the legal basis for the genetic certification of the population of the Russian Federation, the use of the terms «genetic passport», «genetic profile» and «genomic passport», «genomic profile» and provides recommendations for improving the use of relevant terms such as standardizing the requirements for the preparation of a report/conclusion on the results of a genetic study and resolving the issue of the medical nature of the full-genome sequencing process. In addition, the practice of using the term «genetic passport» in federal acts, as well as domestic and foreign literature and media publications, is analyzed. Not only does the paper reveal the concept of complete genome sequencing, but also provides cases of mandatory medical and biological examination, including complete genome sequencing.

Оценка генетического разнообразия популяций Medicago varia Mart. отобранных для селекции в условиях Республики Башкортостан методом SSR-анализа

Medicago varia Mart. (bastard alfalfa) is a highly productive, protein-rich, perennial forage crop, well adapted to the conditions of the Southern Urals and Cis-Urals. In the Republic of Bashkortostan, the breeding of alfalfa is carried out at the Bashkir Scientific Research Institute of Agriculture of the UFRC RAS and the experimental station “Ufimskaya”. To assess the genetic polymorphism of the initial seed material, accurately identify and certify alfalfa varieties, the SSR analysis method can be used, which consists of PCR analysis of the sizes of loci containing microsatellite repeats. Most alfalfa SSR markers have been developed for the model object Medicago truncatula Gaertn. (truncated alfalfa), several studies on the SSR loci of Medicago sativa L (common alfalfa) have been published. For genetic analysis of bastard alfalfa, it is proposed to use the same SSR markers, but how effective they will be on domestic varieties of this species remains unknown. The purpose of this study was to test SSR primers for 10 microsatellite loci on populations of bastard alfalfa, which are in breeding study at the Republic of Bashkortostan. For the study, four samples of M. varia were used: variety Chishminskaya 131, populations Skorospelaya 9, S 3-6, and S 3-8. Analysis of the molecular genetic polymorphism of these M. varia samples using the SSR-PCR method allowed us to obtain data on the allelic composition of the microsatellite loci MsEST53, MSE265, MSE562, MSE486, MSE195, MSE590, MSE323, MsEST9, MSE470, MSE276. The most effective for genetic certification of varieties and populations of this crop were the SSR markers MsEST53, MSE265, MSE562, MSE486, MSE195, MSE590, MsEST9, which gave the largest number of polymorphic DNA fragments according to the results of PCR and polyacrylamide gel electrophoresis, making it possible to distinguish all four samples, and were also characterized by similar primer annealing temperatures and non-overlapping allelic ranges, which makes it theoretically possible to use them in multiplex PCR. The highly variable SSR markers identified during the study can be used to create test systems for accurate identification and certification of varieties, as well as for assessing the genetic polymorphism of M. varia samples.

Caracterização morfológica de novos clones-elites de bananeira

Abstract The characterization of clones is a very important step in genetic certification programs, as it describes and recognizes the plant material at every stage of production, allowing the monitoring of genetic quality, improvement and conservation of the germplasm. The aim of this work was to morphologically characterize two elite banana clones. The experimental design applied was in randomized blocks, with four replications, with six plants per parcel. The treatments consisted of two elite banana clones, Prata Gorutuba R1 and Prata Gorutuba R2 and four commercial cultivars: Prata Gorutuba, Prata Ana, Grande Naine and BRS Princesa. The morphological characterization was carried out in the second production cycle (daughter plant), using 23 qualitative descriptors, visually evaluated, classified according to the instructions for carrying out the distinguishability, homogeneity and stability (DHS) tests of banana cultivars. The elite clones Prata Gorutuba R1 and R2 differed from the cultivars Grande Naine and BRS Princesa regarding the descriptors tapering of the pseudostem, predominant color of the pseudostem, intensity of anthocyanin coloration and color of the underside of the basal sheath. The descriptors made it possible to group elite clones into the Prata group, a group that predominates in crops in Brazil, with characteristics already widely accepted by the market.

The use of SCoT markers for evaluation of the genetic variability of Russian fescue and festulolium varieties

Forage gramineous grasses are the most important component of the hay lands and pasture agroecosystems. To increase the efficiency of grass breeding the complex evaluation of the initial plant material is necessary, including an application of the current DNA technologies. The aim of this study was to investigate the effectiveness of SCoT markers for PCR-analysis of interspecies and intervarietal genetic variations of Russian fescue (Festuca) and festulolium (× Festulolium F. Aschers. et Graebn.) varieties. Total 13 samples, combined 30 seedlings per variety were genotyped with 25 SCoT markers, indicated as informative for gramineous grasses according to literature sources. The high efficiency of SCoT marking technique as a tool for DNA polymorphism revealing was found for Russian fescue and festulolium species and varieties. The obtained results can be used at the varieties identification and genetic certification as well as for selection the parental forms for the breeding process.

Investigation of genetic polymorphism of Russian rape and turnip rape varieties using SSR and SRAP markers.

Rapeseed (Brassica napus L.) and turnip rape (B. rapa L. subsp. campestris (L.)) are important agricultural plants widely used for food, fodder and technical purposes and as green manure. Over the past decades, a large number of perspective varieties that are being currently cultivated in every region of Russia have been developed. To increase the breeding eff iciency and facilitate the seed production, modern molecular-genetic techniques should be introduced as means to estimate species and varietal diversity. The objective of the presented research study was to investigate DNA polymorphism of the rapeseed and turnip rape varieties developed at Federal Williams Research Center of Forage Production and Agroecology and detect informative markers for varietal identif ication and genetic certif ication. To genotype 18 gDNA samples, 42 and 25 combinations of respective SSR and SRAP primers were used. The results obtained demonstrate that SRAP markers were more effective for polymorphism analysis: 36 % of the tested markers revealed genetic polymorphism compared with only 16.7 % of microsatellite loci. Molecular markers to detect differences at interspecif ic and intervarietal levels have also been found. For the investigated set, such microsatellite loci as Na12A02, Ni2C12, Ni02-D08a, Ra02-E01, Ni03H07а and SRAP-marker combinations as F13-R9, Me4- R7, F11-Em2, F10-R7, F9-Em2 and F9-R8 proved to be informative. Application of the two marker techniques made it possible to detect a higher level of DNA polymorphism in plants of different types (spring and winter varieties) if compared against the intervarietal differences within a species or a group. According to Nei’s genetic diversity index, in the cluster of winter rapeseed, VIK 2 and Gorizont varieties had the longest genetic distance, and in the spring cluster, these were Novosel and Veles. A high level of similarity was found between Vikros and Bizon winter rapeseed varieties. The results obtained have a high practical value for varietal specif ication of seed material and genetic certif ication of rapeseed and turnip rape varieties.

Evaluation of microsatellite allelic patterns to DNA fingerprinting in rubber tree clones

The rubber tree (Hevea brasiliensis) is native to the Amazon region, and it is widely exploited due to natural rubber produced from latex. There are many clonal varieties, without certification tests. In order to determine a genetic certification, 15 clones were genotyped to identify their genetic pattern. Ten microsatellites were used to determine a subset of alleles exclusive for each genetic profile. The genetic estimates obtained were: number of alleles per locus (N), expected (HE) and observed (HO) heterozygosity, Polymorphic Information Content (PIC) and Discriminatory Power (DP). The number of alleles (N) ranged from five to 14, with an average of 9.2. The HE mean (0.80) was higher than HO (0.60), indicating a selection for homozygotes. The locus informativeness was verified with PIC (0.77) and DP (0.90) means showing high polymorphism. The dendrogram represented the formation of three groups related to geographical origin. Clone MDF 180 presented the highest genetic divergence. Two genic pools represented the genetic composition of genotypes. Based on allelic profiles, a set of two microsatellites (A2365 and A2368) was able to distinguish all examined clones. The genetic certification using microsatellite fingerprinting proved to be an alternative to morphological traits.

РОЛЬ ГЕНЕТИКИ В СОВРЕМЕННОЙ МЕДИЦИНЕ

The lecture discusses the role of modern genetics and its significance for medicine, determines the goals of genetics and its structure. It is shown that modern medical genetics is divided into general, clinical and laboratory genetics. Other fields of genetics are genomics, molecular and biochemical genetics, cytogenetics, developmental genetics, oncogenetics and immunogenetics, pharmacogenetics, population genetics, ecological genetics, nutrigenetics, toxico-genetics. It is noted that about 20–40 % of clinic patients have hereditary pathology. The main possibilities of modern genetics, such as human genome sequencing, molecular genetic diagnosis of hereditary pathology, personalized medicine, genetic certification, identification of genetic markers for oncological diseases, determination of individual drug sensitivity using pharmacogenetics methods, gene therapy of previously incurable diseases, medical bioengineer-ing and genome editing. The issues of biological aging of the body and the possibility of prolonging active longevity by the methods of modern genetics are discussed. Conclusions are drawn about the need to introduce knowledge, skills and abilities in the field of clinical genetics propaedeutics, genetic testing and interpretation of its results, treat-ment and prevention using modern genetics methods into the system of higher medical education.

Molecular-genetic research is being carried out in cattle

The article presents the preliminary results of molecular genetic studies of the blood of breeding bulls- producers of domestic Bushuev cattle breed for the purpose of their genetic certification and early prediction of breeding and productive qualities.

Genetic certification of Khakasskaya horse by markers of nuclear and mitochondrial DNA

Genetic certification of Khakasskaya horse by markers of nuclear and mitochondrial DNA

Еvaluation of the genetic diversity of varieties of camelina (Сamelina sativa l.) using SSR markers

Relevance. Camelina (Camelina sativa L.) is a geographically widespread oilseed crop characterized by a high content of unsaturated fatty acids in seed oil and resistance to most stress abiotic and biotic factors. The prospect for the development of camelina culture in agriculture is associated with the production of biofuels and a wide range of technical oils. The creation of new specialized highly productive varieties of camelina is associated with the tasks of the chemical, medical and food industries. Increasing the efficiency of the breeding process needs development of methods for the assessing and selecting of genetic material (lines, cultivars etc.). The study of the genetic diversity of a culture using DNA marking, including the microsatellite SSR markers, is considered as an effective way of the pre-breeding stage of breeding work. The aim of this study was to study the polymorphism and phylogenetic relationships of camelina cultivars using SSR markers.Methods. The object of the study was 18 varieties of camelina of various breeding origin, included in the State Register of Varieties of the Russian Federation. Genetic analysis was carried out by PCR using a set of 8 SSR-markers, followed by detection of products on a genetic analyzer.Results. During the study, 40 alleles were identified, with rather high indicators of the level of polymorphism. A specific marker associated with the winter form of life of camelina was revealed. Cluster analysis with the construction of a dendrogram of genetic similarity showed significant differences in the studied samples. The varieties were divided into two separate clusters — winter and spring forms of camelina. In each of the clusters, varieties were grouped mainly by origin (originator). Further development and use of DNA-marking methods will contribute to increasing the efficiency of the breeding process and the formation of a system of genetic certification of oilseeds.

ГЕНЕТИЧЕСКАЯ ЭПИДЕМИОЛОГИЯ НАСЛЕДСТВЕННОЙ ПРЕДРАСПОЛОЖЕННОСТИ К КЕРАТОКОНУСУ

The survey of the literature devoted to genetic epidemiology of keratoconus and also principles of genetic markers search showed predisposition to this disease suitable for screening test in the course of genetic certification of the population. It was revealed that hereditary predisposition to keratokonus was caused by gene mutations, encoding cellular cycle and metabolism of the keratocytes regulating the activity of tissue proteolytic enzymes, and also mechanisms of natural detoxification. Genes associated with keratoconus are characterized by allelic variation and multiple mutations taking different degrees of association with clinically apparent diseases. It was discovered that genotypes of people from different geographic regions can differ in terms of signs and markers showing predisposition to the disease.

SSR analysis of modern Russian potato varieties using DNA samples of nomenclatural standards

The N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR) is developing new approaches to documentation of national cultivars, taking into account recommendations of the International Code of Nomenclature for Cultivated Plants in parallel with methods of genetic certification. The nomenclatural standard of a particular cultivar represented by a herbarium specimen can be used as a reference for verifying authenticity and uniformity of cultivar specimens obtained from various sources. The verification requires fast and reliable methods for cultivar genotyping. This paper presents protocols for modified methods of DNA extraction, PCR-analysis and SSR-genotyping, which allow potato cultivars identification without the use of expensive reagent kits. A set of ten chromosome-specific microsatellite markers was used to study polymorphisms in 66 modern Russian potato cultivars, as well as in 11 pre-cultivars and breeding clones, represented by nomenclatural standards and voucher specimens, respectively. This subset of 77 specimens has demonstrated a high level of polymorphism in ten studied microsatellite loci. The SSR analysis identified 73 alleles; 7.3 alleles per locus were observed on average, the number of which varied from 3 (STG0025 locus) to 11 (locus StI046). The PIC values varied from 0.544 (STG0025 locus) to 0.836 (StI046 locus). The alleles, unique for this subset, were found at six studied loci. The high level of polymorphism at the SSR loci made it possible to unambiguously identify almost every cultivar, with the exception of the expected coincidence of microsatellite profiles of two cultivars, which are somaclonal variants. Using an optimized set of eight microsatellite markers, the genetic relationships of modern Russian potato cultivars were studied.

MODERN WAYS OF RASPBERRY BREEDING

One of the priority tasks in raspberry breeding is to increase the ecological adaptation of varieties to negative biotic and
 abiotic factors of a particular cultivation region. Common task for all raspberry cultivation regions is the breeding of highly
 productive varieties suitable for mechanized cultivation with high commercial, taste and technological qualities of berries.
 The modern breeding process is characterized by a significant increase in the intensity of selection and the acceleration
 of the breeding process. Biotechnological methods of clonal micropropagation of valuable genotypes, as well as the use of PCR
 for genetic analysis and certification of breeding material, are very encouraging. Scientific integration gives the opportunity
 to speed up the breeding process. This is contributed by the creation of modern breeding and nursery-garden centers, where
 joint research is carried out by breeders, geneticists, biotechnologists, physiologists, virologists and nursery breeders.

Legal regulation of personalized medicine in the agricultural sector: the experience of Russia

This study’s topic’s relevance is due to the rapid development of genetic research, when diagnostics, prevention, and treatment are carried out through the study of nucleic acids and their expression products − RNA and proteins. Predictive (personalized) medicine (PMM) has become a preventive trend in molecular medicine, understood in different ways. However, its generally accepted features recognize the individual nature of treatment (each person’s genome is individual). The prophylactic focus of medicine (analysis of the genome is possible at any stage of ontogenesis, long before the disease’s onset) is very important. In carrying out genetic certification, the need to find a legal solution to existing or projected problems is actualized. Legal science is designed to address the issues of protecting human rights in the process of genetic certification, countering discrimination, and other possible violations of constitutional values. The issues raised in the article acquire particular importance in the context of the covid-19 pandemic. Mobility and speed of decision-making require an appropriate legal approach to telemedicine, which will provide the population with high-quality and professional medical care. Besides, it seems reasonable to observe the balance of human rights and freedoms when using the institution of genetic certification and telemedicine

The experience of genetic certification of ash using microsatellite markers

The experience of genetic certification of ash using microsatellite markers

Formation of a system of genetic certification of linseed

Relevance . The study of the genetic diversity of linseed and the clear identification of cultivars of this crop is an important part of breeding work. DNA marking, including the use of microsatellite SSR markers, is considered to be the most effective method for analyzing genetic polymorphism and improving the efficiency of selection. The purpose of this work was to study the polymorphism of a number of modern cultivars of linseed and develop their genetic passport. Materials and methods . The object of research was 22 varieties of oilseed flax included in the state register, of various breeding origin. The genetic analysis was performed by PCR using a line of 11 SSR markers developed and synthesized by “Syntol” LLC, with subsequent detection of products on a genetic analyzer. Results . In the study sample, 46 alleles were identified. Each sample contained a unique set of alleles. The use of alphanumeric code for SSR markers allowed the formation of genetic passports for each studied cultivar. This will allow accurate genotyping of morphologically difficult to distinguish samples, which shows the possibility of certification of all flax cultivars included in the State register of breeding achievements of the Russian Federation. Cluster analysis with the construction of a dendrogram of genetic similarity revealed differences in the studied samples. Cultivars of the studied samples were divided into three separate groups, two of which are characterized by origin and relationships between them, the third group of cultivars are the results of selection work using samples of different geographical origin.

Молекулярно-генетический анализ новых изолятов вируса гриппа птиц субтипа H3N8, выделенных в северных регионах казахстана

Molecular and genetic analysis of viral isolates genes will allow to estimate the spread of influenza A virus in the territory of the Republic of Kazakhstan. Avian influenza control is difficult due to the high variability of the virus genome. The influenza virus circulation among wild waterfowl and the proximity of humans to their habitats is a potential source of threat to public health. Currently, the influenza agent is the subject of detailed study, especially in terms of genetic certification of strains used for the development of diagnostic and prophylactic agents. The aim is studying the molecular genetic properties of new isolates of avian influenza virus subtype H3N8 isolated during the monitoring of avian influenza in the Northern regions of Kazakhstan. Modern methods of molecular biology and genetic engineering were used in the research. In 2018, virological monitoring of wild birds in the Northern regions of Kazakhstan revealed individuals infected with influenza a virus. Pharyngeal swabs of two birds in particular shovelers (Anas clypeata) and teal cracker (Anas querquedula) showed positive reactions for influenza virus type A, subtype H3N8 by PCR. The study obtained isolates of influenza virus A/shoveler/SKO/20/2018 (H3N8) and A/Teal cracker/RMS/45/2018 (H3N8). Results of determining nucleotide sequences and phylogenetic analysis of the new isolates important genes, A/shoveler/SKO/20/2018 (H3N8) and A/Teal cracker/RMS/45/2018 (H3N8) influenza virus in birds are shown. New Kazakhstan isolates of avian influenza virus on the composition of M-gene show the greatest affinity with the strains of avian influenza virus subtype H3N8 isolated in Mongolia in 2018. The molecular genetic analysis results of new isolates of the H3N8 subtype avian influenza virus isolated in the Northern regions of Kazakhstan will be used in the new generation of vaccines production, diagnostics and development of measures to improve the influenza epizootic situation in Kazakhstan. Key words: genetic analysis, avian influenza virus, wild birds, PCR, RNA