The phenomenon of loss of expression of transferred genes in transgenic plants was discovered in the early 1990s. The study of this phenomenon revealed dependence of the frequency of gene silencing on the number of integrated copies in the plant genome, the properties of the transgene sequence itself (the presence of duplications, vector sequences, and others), chromosomal position. Loss of gene expression can occur transcriptionally or post-transcriptionally in most cases involving small interfering RNA (siRNA). In plants, the most common mechanism for inactivation of genes at the level of RNA transcription is RNA-directed DNA methylation (RdDM). An important role is played by the plant-specific RNA polymerase IV and V. Pol IV is assumed to transcribe non-coding transcripts at its target loci. They are copied into long dsRNAs and are processed by DICER into siRNAs. siRNAs are then methylated and loaded into the effector complex, whose main component is a protein of the Argonaute family. RNA polymerase V also transcribes the noncoding transcript of the target gene, but it serves as a scaf¬fold that interacts with siRNAs and that recruits proteins and enzymes responsible for DNA and histone methylation. Posttranscriptional gene inactivation occurs in the cytoplasm and is associated with a specific effector complex (AGO-siRNA), which cleavages homologous mRNA. In plants, in addition to the canonical pathway, RdDM, more mechanisms exist, which include components for posttranscriptional gene inactivation, specific proteins and other types of small RNAs. In this review, we briefly discuss the currently known components of epigenetic regulation.

There are a number of problems in selection of cultivated cereals associated with the requirements to create forms with resistance to diseases, pests and unfavorable environmental conditions. The genetic diversity of genes for resistance to biotic and abiotic stresses can be increased by means of the gene pool of wild and cultivated wheat relatives. To improve agronomic traits in cereals, we have developed common wheat hybrid lines T. aestivum/ T. durum, T. aestivum/ T. dicoccoides and triticale lines by crossing hexaploid triticale with common wheat forms with the substitution of genome D for the geno­me of diploid Aegilops species. The aim of the study was to identify the lines of common wheat and hexaploid triticale with alien introgression using cytological and molecular-genetic analyses and evaluation of their cytological stability. Comparative analysis of the structure of chromosomes by GISH and FISH methods, microsatellite- and chromosome-specific markers revealed that hybridization of triticale with genome-substitution forms of wheat leads to the reorganization of the genome, including both the introgression of foreign material and wheat chromosome rearrangements, which lead to new combinations of genetic loci. The efficiency of wheat microsatellite markers to characterize of the T. aestivum/ T. durum, T. aestivum/ T. dicoccum interspecific hybrid lines was shown. From 4 to 12 translocations of different lengths from T. durum and T. dicoccum were identified in the chromosomes of A and В genomes in the hybrid lines. Meiotic stability of wheat and triticale hybrids was found. It creates prerequisites for preservation of alien genetic material in subsequent generations.

A unique feature of plants is the presence of two extranuclear genomes, chloroplasts and mitochondria. The chloroplast genome is relatively small, 100–120 genes, which encode less than 5 % of all proteins required for plastids to function. The cpDNA expression retains prokaryotic features, cotranscription in the operon, bacteria-like RNA polymerases and promoters, 70S ribosomes etc., also new characters appear such as uncoupling of transcription with translation, phage-type RNA polymerases, RNA editing, and splicing of primary transcripts. The interaction of the nucleus (nuclear genomes) and cytoplasm (plastid and mitochondrial genes) during plant development is necessary for proper development and adaptation to the environment. The aim of this review is to disclose the peculiarities of plastid genome expression. The way the genetic information in chloroplasts is used (transcription, editing, splicing, polyadenylation and translation) is consequently described. Furthermore, the importance of all expression machinery components in plant life is discussed. Modern approaches for RNA pool study are described and critical points of nuclear-cytoplasmic interaction in the functions of chloroplasts are revealed. The information about the most important factors of nuclear-cytoplasmic signaling in higher plants (sigma factors and PPR proteins encoded by the nucleus) are reviewed. Thus, the multilevelness and viability of plastid genome expression regula­tion in plant cells and interdependence of the pro­cesses in different compartments is proved. A summary of the latest studies of the expression of the plastid genome using genetic chips (microarrays, macroarrays) is provided. Original results are presented.

Identification of cytoplasm types with the use of molecular markers enables to simplify the parent line pair selection for hybrid development based on CMS. Forty accessions of the family Brassicaceae (Brassicaceae Burnett) were analyzed with 22 pairs of PCR primers taken from previous research. Seven types of cytoplasm (Ogura, Ogu-NWSUAF, nap, pol, cam, rad, ole) were observed among breeding accessions using standard and multiplex PCR technique. The sequence of PCR products that differentiated different types of sterile cytoplasm confirmed the presence of three genes, orf138, orf222, and orf224, in mitochondrial DNA associated with exhibition of CMS. The accession of Nappa cabbage (Brassica rapa Pekinensis Group) had two genes, orf138 and orf222, which corresponded to cytoplasm Ogu-NWSUAF. All accessions carrying Ogura cytoplasm had the 417 bp fragment, which was 100 % identical to the mitochondrial orf138 gene sequence corres- pon­ding to Type А (formerly nine sequence Types, from A to I, had been identified). An exception was the accession of white head cabbage Tekila F1 with a new allelic variant of orf138 gene, which combined the 39-bp deletion typical of the Type F orf138 sequence and two nonsynonymous substitutions, A→T and G→A, at positions 95 and 99, respectively.

New types of CMS-inducing cytoplasms cannot be applied to hybrid sorghum breeding without knowledge of their effects on major biological and commercial plant traits. In our studies of F1 hybrids obtained by crossing of two sets of isonuclear CMS lines (with nuclear genomes of cv. Pishchevoye 614 (P614) and Zhelyozyornoye 10 (Zh10)) to two pollen parents (cv. Pishchevoye 35 (P35) and Mercury), we focused our attention on the effects of A3, A4, 9E, and M35-1A cytoplasms on chlorophyll content at different developmental stages of sorghum plants. It was found that hybrids with different types of male-sterile cytoplasm differed in chlorophyll content, and the genotypes of the CMS line and the pollen parent influenced the manifestation of cytoplasmic differences. In the F1 hybrids obtained with CMS lines possessing the P614 genome, sterile M35-1A cytoplasm increased chlorophyll a content, in comparison to 9E cytoplasm. In the F1 hybrids obtained with CMS lines with the Zh10 genome and the P35 pollen parent, sterile A4 cytoplasm increased the sum of chlorophyll a and b, in comparison to A3 and 9E cytoplasms, whereas no differences were recorded in the F1 hybrids obtained with Mercury. The F1 hybrids obtained with CMS lines with the P614 genome showed heterosis for total chlorophyll content at the tillering stage. Overdominance of this trait was observed in hybrids with M35-1A cytoplasm; true heterosis exceeded analogous indices in 9E cytoplasm by 19.0 %, and the hypothetical heterosis, by 20.6 %. These data demonstrate that the application of new types of CMS-inducing cytoplasms allows raise of F1 hybrids with heterosis for chlorophyll content. Thus, such types can be used to increase hybrid productivity.

Diverse patterns of plant fruit and seed coloration are determined by the presence of two main types of pigment, carotenoids (red, orange and yellow color) and anthocyanins (purple, blue, red). Thеy belong to two groups of secondary metabolites, isoprenoids and flavonoids. Interest towards the genetic mechanisms that control coloration in plants has recently increased due to the antioxidant and antimicrobial properties of some pigments and their colorless precursors consumed with plant-derived food. The genes encoding enzymes involved in step-bystep conversion of initial organic molecules to final pigmented compounds are referred to as structural genes, while regulatory genes are responsible for activation of the expression of structural genes and control the synthesis of pigments at certain times and in proper tissue. The data in plant genetics accumulated to date show that the inter- and intraspecies phenotypic diversity in coloration is mainly related with regulatory genes. Previously developed rich gene collections and precise genetic models for coloration traits in dicots and monocots as well as the rapid development of molecular genetic methods for studying plants allowed for studying genetic regulation of pigment synthesis at a molecular level. The peculiarities of the regulation of carotenoid biosynthesis are exemplified with Solanaceae fruits. The genetic mechanisms underlying the synthesis of various flavonoid pigments are exemplified with a study of seed color in Poaceae plants. In summary, prospects for the practical use of regulatory genes that control pigment synthesis are discussed and examples of their practical use in vegetable and cereal crop breeding are given.

Alien hybridization in cereals is used for comparative investigations of genome structure and evolution as well as for extracting useful genes from the wild gene pool. The tetraploid species Triticum timopheevii has long been used as a source of genes for resistance to fungal diseases. Line 821 was developed on the genetic background of cultivar Saratovskaya 29 (S29), which is drought-resistant but is very susceptible to diseases and carries big introgressions in 2A and 2B chromosomes and a small introgression in the subtelomeric region of 5A chromosome. The two genotypes were compared for the parameters associated with direct and indirect reaction of the photosynthetic apparatus to water stress. In flag leaves of 821 line, an increased transpiration rate and stomatal conductance (1.6 times the value in optimal watering and 1.2 times the value under water deficit) and, correspondingly, reduced water use efficiency were found compared to the initial cultivar. Additionally, the actual effectiveness and electron transport rate of photosystem II and chlorophyll and carotenoid content were reduced as well as the total antioxidant capacity (approximately three-fold) under water stress. Under the same conditions, lipoxygenase activity was increased two-fold. On the whole, water deficit tolerance was decreased in the line in comparison with the parental cultivar and was accompanied by leaf senescence. Thus, it may be supposed that 2A, 2B and 5A chromosomes of the drought-tolerant cultivar S29 carry important genetic factors responsible for reaction to water stress in wheat plants.

The structures of Picea ajanensis populations were compared based on allozyme analysis of vegetative buds and morphometric analysis of generative organs. Six cenopopulations of P. ajanensis were investigated in areas with various levels of volcanic impact in the Kamchatka Peninsula. The genetic structures of spruce populations and phenotypes were determined by analysis of ten enzyme systems (PGM, GOT, HK, LAP, MDH, SKDH, IDH, GDH, PGI and SOD). Phenotypic variability of spruce populations was estimated based on the composition of morphotypes that were identified by using geometric morphometrics of cone-scale shapes. Pairwise comparison of samples of cones from 170 trees from six populations revealed 12 morphotypes differing in the shape of cone scales. Comparative assessment of variability and similarity of populations was carried out based on the frequency of occurrence of phenotypes and frequency of alleles of polymorphic loci. Correlations of the genetic and phenotypic distance matrices between different phenotypes were revealed. This observation was consistent with the genetic determination of the shape of cone scales in spruce. Genetic differences between the morphotypes with regard to nine polymorphic loci (Got-2, Skdh-1, Idh-2, Pgm-2, Mdh-1, Mdh-3, Pgm- 1, Pgi-2, and Hk) were not significant. Statistically significant differences between the morphotypes were revealed for two loci: Pgm-2 and Mdh-1. Differences in the genetic diversity of spruce populations generally corresponded to differences in their phenotypic diversity. The high levels of genetic and phenotypic diversity characterized a stable population structure of spruce in the area of weak volcanic influence. Changes in the genetic structure and low levels of the phenotypic diversity of spruce were observed under catastrophic volcanic impact.

The fearful withdrawal response to humans was studied with regard to the effect of hereditary and environmental factors in four consecutive generations of minipigs bred at the Institute of Cytology and Genetics. Variation in the withdrawal response was tested in four heterotypic settings. The standard aversive stimulus was the presence of a human as the animals were being given food either as a group or one by one after 14–16 or 2 h of food deprivation. All factors studied are ranged with regard to their contributions to the overall phenotypic variation of the response as follows: sex (0.0–0.4 %), age (0.1–4.7 %), social isolation (0.1–2.1 %), colour types (2.9–7.8 %), boar genotype (10.8 %), food motivation (6.1–12.8 %), and the genotype–food motivation interaction (2.7–56.4 %). That was the first demonstration of hereditary polymorphism of this behavioral reaction in minipigs, which includes three classes of behavioral phenotypes. Sex and age do not affect the withdrawal response in piglets from 1.5-month age to 4.1-month age. It was found that the age-related changes in the behavior of sows depend on the indirect selection of individuals with a quiet phenotype, and the frequency of this phenotype increases from 29 % (the rearing stock) to 63 %. Social isolation and food motivation significantly influence the response in piglets at ages of 1.5 and 4.1 months, but not in sows at ages of 10.4 and 22.5 months. An adverse consequence of the environmental influence of food motivation and its interaction is a broad variability (CV 95–120 %) of the withdrawal response. The results will contribute to the study of the genetics of the fearful-defensive response to humans and to correction of the method for evaluating this behavior, valuable for breeding, in ICG minipigs.

In mammals, males are typically larger and heavier than females. In particular, the average weight of wild boar females is about 80% of that of the males. In a vast majority of domestic swine populations (breeds, populations of breeding groups), this value varies from 70 to 91% (the central value of the range of variation of 81%). However, there are three genealogically continuous groups of domestic pigs (Vietnamese Masked breed MY, minisibs and Svetlogorsk mini-pigs) that make exceptions. Their specific feature is the reverse sexual dimorphism in weight – mature females are heavier than males. This phenomenon, not typical of the species Sus scrofa, was the reason for the present study. Although this research is preliminary, some assumptions can be made. Firstly, the ratio of the weight of mature females to the weight of mature males is obviously characteristic of the species, deviations from which repressed stabilizing selection. Second, in domestic pigs, normal and reverse sexual dimorphism in weight may be different in nature: in the former case, it is a great length of the period of intensive growth in males, in the latter, a large growth rate of females during the first year of life. The third characteristic of domestic pigs in Southeast Asia, early puberty, may be due to a consistent use of young and therefore small-sized males for reproduction purposes; however, the small size due to their youth, cannot be a target of artificial selection – nor can they be the cause of reverse sexual dimorphism in weight. Finally, reverse sexual dimorphism may be due to a tendency towards early obesity in females, which might be to a single mutation as its genetic cause.

History of rye (Secale cereale L.) breeding began from the first targeted selections made in Germany by the Probsteier Seed Cooperative around 1850, and over 150 years breeding yielded a tremendous amount of results. Rye has also long been used as cytological subject due to its low number of chromosomes and their size. However, genetic findings in rye up to the early 1980s were rather scant. About 120 genes could be assigned to seven linkage groups. Only through the development of new methods such as C-banding, in situ DNA hybridization, enzymology and molecular marker techniques achieved an enormous progress. Particularly, the latter was driven by agronomic success of hybrid breeding in rye. The basic genetic knowledge resulted from intra- and interspecies genetic diversity assay and phylogenetic studies in the genus Secale using nuclear and cytoplasmic molecular markers facilitated successful selection of parents for hybrid breeding and hence contributed to improvement of heterosis effects. Main achievements in rye hybrid breeding and genetic mechanisms exploited for different hybrid breeding strategies are discussed. The utilsation of landraces and wild relatives via advanced backcross procedures, combined by QTL analysis and introgression libraries, contributed to increase of heterotic effects. Those marker-assisted approaches became the basis of recent hybrid breeding of rye. Prediction of hybrid performance can also be improved significantly by marker-assisted selection and genomic selection based on genomewide marker data. The findings in rye genetics (including phylogenetic, mapping and population studies) are reviewed in their relation with the hybrid breeding purposes and demands. Overall, about 450 morphological and biochemical traits are mapped throughout the genome plus about 5,000 DNA markers. They are not only associated with individual chromosome or segments but also efficiently used for comparative mapping (evolutionary studies) introgression monitoring, QTL tagging, and marker-assisted selection.

Falling number (FN) reflects the level of alpha amylase activity in grain. The main factor responsible for high α amylase levels and low FN values is visible or hidden preharvest sprouting (PHS) under adverse weather conditions. In recent decades, great progress has been made in the understanding of biochemical and molecular processes accompanying PHS and the genetic control of preharvest sprouting resistance (PHSR) and FN, as well as in the development of methods of breeding for PHSR and FN. However, breeding for these traits and the corresponding theoretical studies have not yet been properly developed or reflected in the Russian literature. The purpose of the review is to fill this gap. It illustrates the genetic complexity and context dependence of the PHSR and FN traits and of major factors impairing FN. A specific feature of breeding for high PHSR and FN is that it involves elimination of late maturity α-amylase (LMA) genotypes in choosing parents for crossing and from early hybrid generations; choice of donors of target traits with regard to their genetic diversity; methods of evaluation of varieties and lines for PHSR and FN under different environmental conditions; determination of F2 population size with regard to combination of PHSR, FN, high performance, grain quality, and other commercial traits. New methods and approaches in breeding open new prospects. They include the doubled haploid (DH) method, allowing homozygotes to be obtained from early hybrid generations; and DNA technologies, which permit genetically reasonable selection of PHSR and FN donors, pyramiding of desirable alleles, and efficient selection of desired offspring using closely linked molecular markers.

The human TRPM8 gene encodes a receptor mediating cold sensitivity, and this fact points to its putative role in cold adaptation. The structural variability of the TRPM8 gene for five single-nucleotide polymorphisms (SNPs) has been studied in Kyrgyz population. The SNPs are located in coding regions of the gene, and three of them are confined to a segment of 20 bp in exon 7. The frequencies of minor SNP alleles are: rs13004520 G/C = 0.06; rs28901637 А/Т = 0.13; rs11562975 G/C = 0.27; rs7593557 G/A = 0.21; rs11563071 С/G = 0.12. The analyzed sample of Kyrgyz population includes 275 individuals living at different altitudes and under drastically different climatic conditions. The frequency of the minor rs11562975 allele in highlanders (living above 2 800 m A. S. L.) is one-third lower than in residents of lower regions (760–2 800 m A. S. L.; p < 0.01). This result presumes a selective role of rs11562975 in cold adaptation. Comparison of haplotype frequencies in Kyrgyz people with Europeans, East Asians, and Africans shows a clear narrowing of genotype variation in Europeans in comparison to all others. Probably, this phenomenon is related to a population size decline (bottleneck effect) during the evolution. We consider the exon– intron structure of the TRPM8 gene. Epigenetic markers in the vicinity of the gene have been analyzed. Two strong binding sites for insulator ctcf proteins are present there. They are likely to be associated with chromatin conformation and alternative splicing regulation. A structure–functional characterization of genes for the TRP protein family is provided.

HRAS, KRAS and NRAS gene products belong to the superfamily of small GTPases. These proteins regulate cellular response to extracellular stimuli by means of activation of different signaling pathways. Although the role of RAS gene mutations in the pathogenesis of various human cancers has been established, the clinical significance of these molecular alterations in bladder cancer remains unclear. The aim of this study was to determine the frequency and spectrum of HRAS, KRAS and NRAS mutations, to analyze their relationships with clinicopathological variables and to determine the prognostic value of these alterations in terms of recurrence, progression and mortality, in a prospective cohort of 249 bladder cancer patients. The frequency of RAS mutations detected by the SNaPshot method, was found to be 11.2 %, of which HRAS mutations accounted for 64.3 %, KRAS, for 28.6 % and NRAS, for 7.1 %. We failed to find any correlation between all RAS mutations and pathomorphological characteristics. However, when analyzed separately, HRAS and KRAS mutations were for the first time shown to be associated with the opposite clinical parameters of bladder cancer: HRAS mutations were significantly associated with low-stage low-grade papillary tumors of a small size (р < 0.05), whereas KRAS mutations were associated with non-papillary urothelial carcinomas and the presence of metastasis (р < 0.05). Analysis of the prognostic value of molecular alterations revealed an association of KRAS mutations with decreased cancer-specific survival in both the whole group of patients and the subgroup with non-muscle invasive disease. The data obtained suggest that HRAS and KRAS gene mutations may characterize alternative pathways of bladder cancer pathogenesis: HRAS mutations indicating benign and KRAS mutations, aggressive disease course.