The genus ElymusL., together with wheat, rye, and barley, belongs to the tribe Triticeae. Apart from its  economic value, this tribe is characterized by abundance of polyploid taxa formed in the course of remote hybridization. Single-copy nuclear genes are convenient markers for identification of source genomes incorporated into  polyploids. In the present work, a CAPS-marker is developed to distinguish basic St, H, and Y genomes comprising  polyploid genomes of Asiatic species of the genus Elymus. The test is based on electrophoretic analysis of restriction patterns of a PCR-amplified fragment of the gene coding for beta-amylase. There are about 50 Elymusspecies  in Russia, and most of them are supposed to possess one of three haplome combinations, StH, StY and StHY. Boreal  StH-genomic species endemic for Russia are the least studied. On the basis of nucleotide sequences from public  databases, TaqI restrictase was selected, as it produced patterns of restriction fragments specific for St, H, and Y  haplomes easily recognizable in agarose gel. A sample of 68 accessions belonging to 32 species was analyzed.  In 15 species, the earlier known genomic constitutions were confirmed, but in E. kamojithis assay failed to reveal  the presence of H genome. This unusual H  genome was suggested to originate from a different Hordeum species. In 16 species, genomic constitutions were identified for the first time. Fifteen accessions from Asian Russia  possessed the genomic constitution StStHH, and E. amurensis, phylogenetically close to the StY-genomic species  E. ciliaris, had the genomic constitution StStYY. It is inferred that the center of species diversity of the StH-genomic  group is shifted to the north as compared to the center of origin of StY-genomic species, confined to China.

Molecular and biochemical markers are used to analyze the intraspecific genetic diversity of crops.  Prolamincoding loci are highly effective for assessing this indicator. On the basis of the Laboratory of Varietal  Seed Identification of the State Agrarian University of the Northern Trans-Urals, 18 varieties of common oat  included in the State Register of Selection Achievements in the Tyumen Region from the 1930s to 2019 were  studied by electrophoresis in 2018–2019. The aim of the work was to study the dynamics of the genetic diversity  of oat va rieties at avenin-coding loci. For the analysis, 100 grains of each variety were used. Electrophoresis was  carried out in vertical plates of 13.2 % polyacrylamide gel at a constant vol tage of 500 V for 4.0–4.5 h. It was found  that 44.4 % of the varieties are heterogeneous, each consisting of two biotypes. For three loci, 20 alleles were  identified, 10 of which were detected for the first time. The allele frequency of avenin-coding loci varied with  time. In the process of variety exchange, alleles that are characteristic of varieties of non-Russian origin were replaced by alleles present in domestic varieties and then in the varieties developed by local breeding institutions.  The following alleles had the highest frequency in Tyumen varieties: Avn A4(50.0 %), A2(25.0 %), Avn B4(50.0 %),  Bnew6(37.5 %), Avn C1(37.5 %), C2 and C5(25.0 %). These alleles are of great value as markers of agronomically  and adaptively important characters for the region in question. The amount of genetic diversity of oats varied  with time from 0.33 in 1929–1950 to up to 0.75 in 2019. The high value of genetic diversity in modern breeding  varieties of the Scientific Research Institute of Agriculture of the Northern Trans-Urals and an increase in this  indicator over the past 20 years are associated with the use of genetically heterogeneous source material in the  breeding process. This allowed obtaining varieties with high adaptive potentials in the natural climatic conditions of the region.

Stem rust in recent years has acquired an epiphytotic character, causing significant economic damage  for wheat production in some parts of Western Siberia. On the basis of a race composition study of the stem rust  populations collected in 2016–2017 in Omsk region and Altai Krai, 13 pathotypes in Omsk population and 10 in  Altai population were identified. The race differentiation of stem rust using a tester set of 20 North American  Sr genes differentiator lines was carried out. The genes of stem rust pathotypes of the Omsk population are avirulent only to the resistance gene Sr31, Altai isolates are avirulent not only to Sr31, but also to Sr24, and Sr30. A low  frequency of virulence (10–25 %) of the Omsk population pathotypes was found for Sr11, Sr24,Sr30, and for Altai  population – Sr7b,Sr9b,Sr11,SrTmp, which are ineffective in Omsk region. Field evaluations of resistance to stem  rust were made in 2016–2018 in Omsk region in the varieties and spring wheat lines from three different sources.  The first set included 58 lines and spring bread wheat varieties with identified Sr genes – the so-called trap nursery  (ISRTN – International Stem Rust Trap Nursery). The second set included spring wheat lines from the Arsenal collection, that were previously selected according to a complex of economically valuable traits, with genes for resistance  to stem rust, including genes introgressed into the common wheat genome from wild cereal species. The third  set included spring bread wheat varieties created in the Omsk State Agrarian University within the framework of  a shuttle breeding program, with a synthetic wheat with the Ae. tauschiigenome in their pedigrees. It was established that the resistance genes Sr31, Sr40,Sr2 complexare effective against stem rust in the conditions of Western  Siberia. The following sources with effective Srgenes were selected: (Benno)/6*LMPG-6 DK42, Seri 82, Cham 10,  Bacanora (Sr31), RL 6087 Dyck (Sr40), Amigo (Sr24,1RS-Am), Siouxland (Sr24,Sr31), Roughrider (Sr6, Sr36), Sisson  (Sr6,Sr31,Sr36), and Fleming (Sr6,Sr24,Sr36,1RS-Am), Pavon 76 (Sr2 complex) from the ISRTN nursery; No. 1 BC 1F2 (96 × 113) × 145 × 113 (Sr2,Sr36,Sr44), No. 14а F 3(96 × 113) × 145 (Sr36,Sr44), No. 19 BC 2F3(96 × 113) × 113 (Sr2, Sr36, Sr44), and No. 20 F 3 (96 × 113) × 145  (Sr2,Sr36,Sr40, Sr44) from the Arsenal collection; and the Omsk State Agrarian  University varieties Element 22 (Sr31,Sr35), Lutescens 27-12, Lutescens 87-12 (Sr23,Sr36), Lutescens 70-13, and  Lutescens 87-13 (Sr23,Sr31,Sr36). These sources are recommended for inclusion in the breeding process for developing stem rust resistant varieties in the region.  

The Septoriablotch of spring wheat leaves and ears is one of the most economically significant infections in the Siberian region. In the control systems of Septoriablotch the main ecologically safe element is resistant  varieties, which are designed to slow down the pathogens reproduction rate and slow down or stop the development of the epiphytotic process. The purpose of the work was to clarify the species composition of Septoriablotch  pathogens for West Siberian regions and spring wheat varieties, to study the epiphytotic process of Septoriadifferentially on the leaves and ears of varieties, and to evaluate the activity of seed transmission of Parastagonospora  nodorum. Studies were carried out in 2016–2018 according to generally accepted methods. Septorialeaf and ear  blotch of spring wheat is widespread in West Siberia and the Trans-Urals, causing a decrease in yield by up to 50 %  or more with the deterioration in grain quality. The causative agents of the disease are P. nodorum, Septoria tritici,  and P. avenaef. sp. triticae, and the species ratio varied across the regions and varieties, and within plant organs.  In Novosibirsk Region, P. nodorumcompletely dominated; S. triticiwas 13.8 times less common; and P. avenae f. sp. triticaewas a singleton. In Tyumen Region, the dominance of P. nodorumwas disrupted in some geographic  locations by S. triticiand P. avenaef. sp. triticae. In Altai Krai, P. nodorumpredominated at all points studied; S. tritici and P. avenaef. sp. triticaewere found everywhere, but 5.6 and 8.6 times less often, respectively. The study of spring  wheat varieties of different origins has not revealed any samples immune to Septoriablotch. A differen tiated manifestation of resistance to Septorialeaf and ear disease has been established. Some varieties show complex resistance, combining reduced susceptibility to Septorialeaf and ear disease. Seed infection with P. nodorumin the  regions of Siberia reached 7 thresholds and was largely (52.5 %) determined by the August weather conditions.  The study of the collection of spring wheat varieties from three Siberian regions has revealed the following trend.  Transmission of P. nodorumwith the seeds of varieties was the most active (7.6 %) in Novosibirsk Region and somewhat weaker in Omsk Region (5.7 %). The most favorable phytosanitary situation was in Kurgan Region, where  varieties transmitted P. nodorumto a low degree (2.1 %), below the threshold.

Methylotrophic yeasts have been used as the platform for expression of heterologous proteins since the  1980’s. They are highly productive and allow producing eukaryotic proteins with an acceptable glycosylation level.  The first Pichia pastoris-based system for expression of recombinant protein was developed on the basis of the treeexudate-derived strain obtained in the US southwest. Being distributed free of charge for scientific purposes, this system has become popular around the world. As methylotrophic yeasts were classified in accordance with biomolecular  markers, strains used for production of recombinant protein were reclassified as Komagataella phaffii. Although patent  legislation suggests free access to these yeasts, they have been distributed on a contract basis. Whereas their status  for commercial use is undetermined, the search for alternative stains for expression of recombinant protein continues.  Strains of other species of methylotrophic yeasts have been adapted, among which the genus Ogataearepresentatives prevail. Despite the phylogenetic gap between the genus Ogataeaand the genus Komagataellarepresentatives, it turned out possible to use classic vectors and promoters for expression of recombinant protein in all cases. There  exist expression systems based on other strains of the genus Komagataellaas well as the genus Candida. The potential  of these microorganisms for genetic engineering is far from exhausted. Both improvement of existing expression systems and development of new ones on the basis of strains obtained from nature are advantageous. Historically, strains  obtained on the southwest of the USA were used as expression systems up to 2009. Currently, expression systems  based on strains obtained in Thailand are gaining popularity. Since this group of microorganisms is widely represented  around the world both in nature and in urban environments, it may reasonably be expected that new expression systems for recombinant proteins based on strains obtained in other regions of the globe will appear.

Arbuscular mycorrhiza fungi (AMF) form one of the most common symbiosis with the majority of land plants. AMF supply the plant with various mineral elements, primarily phosphorus, and improve the water supply. The search for the most effective AMF strains for symbiosis and the creation of microbial preparations on that basis is an important task for modern biology. Owing to the difficulties of cultivation without a host plant and their high genetic polymorphism, identifying AMF is very difficult. The high number of cryptic species often also makes morphological identification unreliable. Recent years have seen growth in the number of AMF biodiversity studies performed by modern NGS-based methods, Illumina MiSeq in particular. Currently, there are still many questions that remain for the identification of AМF. The most important are whether conservative or variable sequences should be used to select a marker for barcoding and whether universal primers or those specific to AMF should be used. In our work, we have successfully used universal primers ITS3 and ITS4 for the sequencing in Illumina MiSeq of the 5.8S rDNA – ITS2 region of the 35S rRNA genes, which contain both a conservative and variable regions. The molecular genetic approach for AMF identification was quite effective and allowed us to reliably identify eight of nine isolates to the species level: five isolates of Rhizophagus irregularis, and one isolate of R. invermaius, Paraglomus laccatum, and Claroideoglomus etunicatum, respectively. For all five R. irregularis isolates high variability in the ITS region and the absence of ecotopic-related molecular characters in the ITS2 region were demonstrated. The NCBI data is still insufficient for accurate AMF identification of Acaulospora sp. isolates from the genus to the species level.

Intestinal human microbiota is a dynamic system that is under the pressures of its host organism and external factors. Microbiota disruption caused by these factors can lead to severe diseases including inflammatory and oncological diseases of the gastrointestinal tract. One of the possible approaches in managing the intestinal microbiota is fecal microbiota transplantation (FT) – transfer of the microbiota from the stool of a healthy donor to the intestinal tract of a recipient patient. Currently, this procedure is recognized as an efficacious method to normalize the intestinal microbiota mainly in inflammatory diseases of the gastrointestinal tract. In Russia, pilot studies of the effectiveness of FT in patients with ulcerative colitis have been conducted for several years, and these studies were started in Novosibirsk. The aim of this study was to assess the change of intestinal microbiome in 20 patients with ulcerative colitis after a single FT procedure. The main method is a comparative analysis of 16S ribosomal RNA sequence libraries constructed using fecal samples obtained from patients with ulcerative colitis before and after FT and sequenced on the Illumina MiSeq platform. The obtained results showed that FT led to an increase in average biodiversity in samples after FT compared to samples before FT; however, the difference was not significant. In the samples studied, the proportion of Firmicutes sequences, the major gastrointestinal microbiota of healthy people, was decreased (~32 % vs. >70 %), while the proportion of Proteobacteria sequences was increased (>9 % vs. <5 %). In some samples collected before FT, sequences of pathogenic Firmicutes and Proteobacteria were detected, including Acinetobacter spp., Enterococcusspp., Klebsiella pneumoniae, Proteus mirabilis, Staphylococcus aureus, Stenotrophomonas maltophylia, Streptococcusspp. In most cases, the proportion of such sequences after FT substantially decreased in appropriate samples. The exception was the Clostridiumdifficilesequences, which accounted for <0.5 % of the sequences in samples from almost half of the patients and after FT, the share of such C. difficilesequences was significantly reduced only in samples from three patients. It should be noted that the proportion of Lactobacillusspp. increased ten-fold and their species composition significantly expanded. According to the obtained results, a preliminary conclusion can be made that even a single FT procedure can lead to an increase in the biodiversity of the gastrointestinal microbiota in patients and to the optimization of the taxonomic composition of the microbiota.

This review presents the current progress in and approaches to in vitroconservation of reproductive cells of animals, including birds, such as cryopreservation and freeze-drying, as well as epigenetic conditions for re storing viable spermatozoa and female gametes after conservation. Cryopreservation is an effective way to preserve reproductive cells of various species of animals and birds. In vitrogene pool conservation is aimed primarily to the restoration of extinct breeds and populations and to the support of genetic diversity in populations prone to genetic drift. It is the combination of ex situ in vivoand ex situ in vitromethods that can form the basic principles of the strategy of animal genetic diversity preservation. Also, use of cryopreserved semen allows faster breeding in industrial poultry farming. Despite numerous advances in semen cryobiology, new methods that can more efficiently restore semen fertility after cryopreservation are being sought. The mechanisms underlying the effect of cryopreservation on the semen parameters of cocks are insufficiently understood. The review reflects the results of recent research in the field of cryopreservation of female and male germ cells, embryonic cells, the search for new ways in the field of genetic diversity in vitro (the development of new cryoprotective media and new conservation technologies: freeze-drying). Molecular aspects of cryopreservation and the mechanisms of cryopreservation influence on the epigenetic state of cells are highlighted. Data on the results of studies in the field of male reproductive cell lyophilization are presented. The freeze-drying of reproductive cells, as a technology for cheaper access to the genetic material of wild and domestic animals, compared to cryopreservation, attracts the attention of scientists in Japan, Israel, Egypt, Spain, and France. There is growing interest in the use of lyophilized semen in genetic engineering technologies. Methods of freeze-drying are developed taking into account the species of birds. Organizational and legal ways of solving the problems of in vitroconservation of genetic resources of farm animals, including birds, are proposed.

Identifying genome regions that are directly or indirectly associated with developmental defects and malformations in domesticated pigs can help identify genomic traits used as biomarkers of the structural and functional composition of the body, their metabolic status and genetic diseases as well. Such studies are directly related to the improvement of the economic efficiency, as they allow identification and exclusion of defect animals, who may carry target genes not appearing phenotypically, from the breeding process. In the current work, we have searched for these kind of target genes and genome regions with conducting the genome-wide association studies using PorcineSNP60K BeadChips (Illumina, San Diego, USA). A total of 48 boars of a large white breed of the nucleus farm “Znamenskoe” were analyzed for 21 traits of indicated shortcomings of the exterior and defects of development in 39,153 their offspring.  Calculations were made using a mixed type linear model in package GEMMA. In this study, we selected only 36,704 polymorphic SNPs from an initial 61,000-strong SNP set. After GWAS, we obtained 24 alleles in 11 corresponding genes  (P < 0.1) in the genome of pigs, which are significantly correlated with traits of developmental abnormalities such as anal atresia (ARMC7,FANCC,RND3,ENSSSCG00000017216), limb problems (PAWR,NTM,OPCML,ENSSSCG00000040250, ENSSSCG00000017018) and tremor of piglets (RIC3,ENSSSCG00000032665). Also, co-expression of the NTM,OPCMLand  RND3genes was revealed. This study confirms the relevance of using the single SNP detection according to the single trait approach in associative studies, even for small sample numbers.

There is a hypothesis of the involvement of the glutamatergic system in the development of autism. It has been shown that the chronic experience in daily intermale confrontations leads to disturbances in social behavior: a decrease in communicativeness, disturbances of socialization, emergence of stereotypical behaviors that can be considered as symptoms of the autistic spectrum disorders. So, the aim of this study was to investigate changes in the expression of glutamatergic (GG) and autism-related (GA) genes in the hippocampus of animals with impaired social behavior caused by repeated experience of social defeat or aggression in daily agonistic confrontations. To form groups of animals with contrasting behaviors, a model of sensory contact (chronic social stress) was used. The collected brain samples were sequenced at JSC Genoanalytica (http://genoanalytica.ru/, Moscow, Russia). Transcriptomic analysis revealed a down-regulation of autism-related (Shank3, Auts2, Ctnnd2, Nrxn2) and glutamatergic (Grm4) genes in aggressive mice. At the same time, the expression of GA-related genes (Shank2, Nlgn2, Ptcdh10, Reln, Arx) and GG genes (Grik3, Grm2, Grm4, Slc17a7, Slc1a4, Slc25a22) excluding Grin2a was increased in defeated mice. Correlative analysis revealed a statistically significant association between GG and GA expression. These results can serve as a confirmation of the participation of the glutamatergic system in the pathophysiology of the autistic spectrum disorder.

Hypothalamic melanocortin 4 receptors (MC4R) regulate energy balance. Mutations in the MC4R gene are the most common cause of monogenic obesity in humans. Fibroblast growth factor 21 (FGF21) is a promising antiobesity agent, but its effects on melanocortin obesity are unknown. Sex is an important biological variable that must be considered when conducting preclinical studies; however, in laboratory animal models, the pharmacological effects of FGF21 are well documented only for male mice. We aimed at investigating whether FGF21 affects metabolism in male and female mice with the lethal yellow (A^y ) mutation, which results in MC4R blockage and obesity development. Obese C57Bl-A^y male and female mice were administered subcutaneously for 10 days with vehicle or FGF21 (1 mg per 1 kg). Food intake (FI), body weight (BW), blood parameters, and gene expression in the liver, muscles, brown adipose tissue, subcutaneous and visceral white adipose tissues, and hypothalamus were measured. FGF21 action strongly depended on the sex of the animals. In the males, FGF21 decreased BW and insulin blood levels without affecting FI. In the females, FGF21 increased FI and liver weight, but did not affect BW. In control A^y -mice, expression of genes involved in lipid and glucose metabolism (Ppargc1a, Cpt1, Pck1, G6p, Slc2a2) in the liver and genes involved in lipogenesis (Pparg, Lpl, Slc2a4) in visceral adipose tissue was higher in females than in males, and FGF21 administration inhibited the expression of these genes in females. FGF21 administration decreased hypothalamic POMC mRNA only in males. Thus, the pharmacological effect of FGF21 were significantly different in male and female A^y -mice; unlike males, females were resistant to catabolic effects of FGF21.

The article is about the role of transposons in the regulation of functioning of neuronal stem cells and mature neurons of the human brain. Starting from the first division of the zygote, embryonic development is governed by regular activations of transposable elements, which are necessary for the sequential regulation of the expression of genes specific for each cell type. These processes include differentiation of neuronal stem cells, which requires the finest tuning of expression of neuron genes in various regions of the brain. Therefore, in the hippocampus, the center of human neurogenesis, the highest transposon activity has been identified, which causes somatic mosai cism of cells during the formation of specific brain structures. Similar data were obtained in studies on experimental animals. Mobile genetic elements are the most important sources of long non-coding RNAs that are coexpressed with important brain protein-coding genes. Significant activity of long non-coding RNA was detected in the hippocampus, which confirms the role of transposons in the regulation of brain function. MicroRNAs, many of which arise from transposon transcripts, also play an important role in regulating the differentiation of neuronal stem cells. Therefore, transposons, through their own processed transcripts, take an active part in the epigenetic regulation of differentiation of neurons. The global regulatory role of transposons in the human brain is due to the emergence of protein-coding genes in evolution by their exonization, duplication and domestication. These genes are involved in an epigenetic regulatory network with the participation of transposons, since they contain nucleotide sequences complementary to miRNA and long non-coding RNA formed from transposons. In the memory formation, the role of the exchange of virus-like mRNA with the help of the Arc protein of endogenous retroviruses HERV between neurons has been revealed. A possible mechanism for the implementation of this mechanism may be reverse transcription of mRNA and site-specific insertion into the genome with a regulatory effect on the genes involved in the memory.  

Osteogenesis imperfecta (imperfect osteogenesis in the Russian literature) is the most common hereditary form of bone fragility, it is a genetically and clinically heterogeneous disease with a wide range of clinical severity, often leading to disability from early childhood. It is based on genetic disorders leading to a violation of the structure of bone tissue, which leads to frequent fractures, impaired growth and posture, with the development of characteristic disabling bone deformities and associated problems, including respiratory, neurological, cardiac, renal impairment, hearing loss. Osteogenesis imperfecta occurs in both men and women, the disease is inherited in both autosomal dominant and autosomal recessive types, there are sporadic cases of the disease due to de novomutations, as well as X-linked forms. The term “osteogenesis imperfecta” was coined by W. Vrolick in the 1840s. The first classification of the disease was made in 1979 and has been repeatedly reviewed due to the identification of the molecular cause of the disease and the discovery of new mechanisms for the development of osteogenesis imperfecta. In the early 1980s, mutations in two genes of collagen type I (COL1A1and COL1A2) were first associated with an autosomal dominant inheritance type of osteogenesis imperfecta. Since then, 18 more genes have been identified whose products are involved in the formation and mineralization of bone tissue.  The degree of genetic heterogeneity of the disease has not yet been determined, researchers continue to identify new genes involved in its pathogenesis, the number of which has reached 20. In the last decade, it has become  known that autosomal recessive, autosomal dominant and X-linked mutations in a wide range of genes, encoding  proteins that are involved in the synthesis of type I collagen, its processing, secretion and post-translational modification, as well as in proteins that regulate the differentiation and activity of bone-forming cells, cause imperfect  osteogenesis. A large number of causative genes complicated the classical classification of the disease and, due to new advances in the molecular basis of the disease, the classification of the disease is constantly being improved.  In this review, we systematized and summarized information on the results of studies in the field of clinical and genetic aspects of osteogenesis imperfecta and reflected the current state of the classification criteria for diagnosing the disease.