Conservation of plant genetic diversity, including economically important crops, is the foundation for food safety. About 90 % of the world’s crop genetic diversity is stored as seeds in genebanks. During storage seeds suffer physiological stress consequences, one of which is the accumulation of free radicals, primarily reactive oxygen species (ROS). An increase in ROS leads to oxidative stress, which negatively affects the quality of seeds and can lead to a complete loss of their viability. The review summarizes data on biochemical processes that affect seed longevity. The data on the destructive effect of free radicals towards plant cell macromolecules are analyzed, and the ways to eliminate excessive ROS in plants, the most important of which is the glutathioneascorbate pathway, are discussed. The relationship between seed dormancy and seed longevity is examined. Studying seeds of different plant species revealed a negative correlation between seed dormancy and longevity, while various authors who researched Arabidopsis seeds reported both positive and negative correlations between dormancy and seed longevity. A negative correlation between seed dormancy and viability probably means that seeds are able to adapt to changing environmental conditions. This review provides a summary of Arabidopsis genes associated with seed viability. By now, a significant number of loci and genes affecting seed longevity have been identified. This review contains a synopsis of modern studies on the viability of barley seeds. QTLs associated with barley seed longevity were identified on chromosomes 2H, 5H and 7H. In the QTL regions studied, the Zeo1, Ale, nud, nadp-me, and HvGR genes were identified. However, there is still no definite answer as to which genes would serve as markers of seed viability in a certain plant species.

Microsatellite (SSR) markers with known precise intrachromosomal locations are widely used for mapping genes in rye and for the investigation of wheat-rye translocation lines and triticale highly demanded for mapping economically important genes and QTL-analysis. One of the sources of novel SSR markers in rye are microsatellites transferable from the wheat genome. Broadening the list of available SSRs in rye mapped to chromosomes is still needed, since some rye chromosome maps still have just a few microsatellite loci mapped. The goal of the current study was to integrate wheat EST-SSRs into the existing rye genetic maps and to construct a consensus rye microsatellite map. Four rye mapping populations (P87/P105, N6/N2, N7/N2 and N7/N6) were tested with CFE (EST-SSRs) primers. A total of 23 Xcfe loci were mapped on rye chromosomes: Xcfe023, -136 and -266 on chromosome 1R, Xcfe006, -067, -175 and -187 on 2R, Xcfe029 and -282 on 3R, Xcfe004, -100, -152, -224 and -260 on 4R, Xcfe037, -208 and -270 on 5R, Xcfe124, -159 and -277 on 6R, Xcfe010, -143 and -228 on 7R. With the exception of Xcfe159 and Xcfe224, all the Xcfe loci mapped were found in orthologous positions considering multiple evolutionary translocations in the rye genome relative to those of common wheat. The consensus map was constructed using mapping data from the four bi-parental populations. It contains a total of 123 microsatellites, 12 SNPs, 118 RFLPs and 2 isozyme loci.

Potato (Solanum tuberosum L.) is one of the most important food crops in the world. The genome of this potato species is autotetraploid and has a high level of heterozygosity, also this potato species is a cross-pollinated plant. These characteristics complicate the genetic analysis and breeding process. The tuber’s eye depth is an important trait that affects the suitability of potato varieties for processing. Potato breeding for this trait is based on phenotypic assessment. Identification of the loci that control tuber eye depth would allow diagnostic markers for the marker-assisted selection to be created. The aim of this study is to search for loci associated with the eye depth by analyzing Solanum tuberosum varieties from the GenAgro collection of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, genotyped using the Illumina 22K SNP potato array DNA chip. The 24 significant markers associated with the “eye depth” trait were identified using 15,214 SNP markers genotyped with the Illumina 22K SNP potato array chip and the general linear model (GLM) taking into account the population structure. Data obtained showed the presence of SNPs in four genomic regions: on chromosome 4 (1 marker in the 3.92 Mb area), 5 (1 marker in the 4.67 Mb area) and 10 (1 marker in the 4.87 Mb area and 21 markers in the region between 48.1–48.9 Mb). The results of localization in the region 48.1–48.9 Mb of chromosome 10 correspond to previously published studies, the remaining three regions were detected for the first time. DNA sections containing SNPs linked to the tuber’s eye depth were studied in the SolTub_3.0 potato genome assembly (https:// plants.ensembl.org/). KASP markers were developed based on the data obtained. It will be possible to screen the breeding material and to breed the varieties more effectively using current markers associated with a shallow tuber’s eye depth.

In connection with the development of breeding and the creation of new plant varieties, the problem of their genotyping and identification is becoming increasingly important, therefore the use of molecular methods to identify genetic originality and assess plant genetic diversity appears to be relevant. As part of the work performed, informative ISSR and IRAP DNA markers promising for the study of genetic diversity of the Rosa L. genus were sought and applied to analysis of genetic relationships among 26 accessions of the genus Rosa L. from the gene pool collection of Nikita Botanical Gardens. They included 18 cultivated varieties and 8 accessions of wild species. The species sample included representatives of two subgenera, Rosa and Platyrhodon. The subgenus Platyrhodon was represented by one accession of the species R. roxburghii Tratt. Cultivated roses were represented by varieties of garden groups hybrid tea, floribunda, and grandiflora. The tested markers included 32 ISSRs and 13 IRAPs. Five ISSR markers (UBC 824, ASSR29, 3A21, UBC 864, and UBC 843) and three IRAPs (TDK 2R, Сass1, and Сass2) were chosen as the most promising. They were used for genotyping the studied sample of genotypes. In general, they appeared to be suitable for further use in studying the genetic diversity of the genus Rosa L. The numbers of polymorphic fragments ranged from 12 to 31, averaging 19.25 fragments per marker. For markers UBC 864 and UBC 843, unique fingerprints were identified in each accession studied. The genetic relationships of the studied species and varieties of roses analyzed by the UPGMA, PCoA, and Bayesian methods performed on the basis of IRAP and ISSR genotyping are consistent with their taxonomic positions. The genotype of the species R. roxburghii of the subgenus Platyrhodon was determined genetically as the most distant. According to clustering methods, the representative of the species R. bengalensis did not stand out from the group of cultivated varieties. When assessing the level of genetic similarity among the cultivated varieties of garden roses, the most genetically isolated varieties were ‘Flamingo’, ‘Queen Elizabeth’, and ‘Kordes Sondermeldung’; for most of the other varieties, groups of the greatest genetic similarity were identified. This assessment reflects general trends in phylogenetic relationships, both among the studied species of the genus and among cultivated varieties.

Intragenomic polymorphism of ITS1 and ITS2 of nuclear ribosomal DNA sequences was analysed in 33 samples belonging to the Nitraria species N. schoberi, N. sibirica, and N. komarovii. The nucleotide variability of the ITS region was detected in the Nitraria species as single-nucleotide substitutions (mainly transitions) and single-nucleotide deletion. Information about the nucleotide variability of fragments is given for the first time by us. The ITS1-5.8S-ITS2 region contained 17 phylogenetically informative single-nucleotide polymorphisms. Eleven single-nucleotide substitutions (transitions, C/T) were detected in ITS1. The ITS2 spacer contained 273–274 bp and was more conservative. A total of 5 phylogenetically informative single-nucleotide polymorphisms (4 transitions: C/T, G/A, one transversion: G/C), one single-nucleotide deletion (T/–) were detected in ITS2. The average GC content was 61.5 %. The GC content was lower in N. sibirica (59.2 %) than in N. schoberi and N. komarovii (62.7 %). It has been shown that the shorter ITS2 is a suitable molecular marker separating these species, due to the low interspecific variability and simultaneous available intraspecific variability. Phylogenetic ML and BI trees constructed separately for the ITS1 and ITS2 spacers, as well as separately for the full-size ITS region and the ITS2 spacer, were congruent. The results obtained on the intraspecific differentiation of N. sibirica revealed two main ribotypes among the samples of this species: the main Siberian sibirica-ribotype and the main Kazakh sibiricaribotype. Geographical features of the distribution of N. sibirica ribotypes, as well as the presence of significant differences between the main Siberian and Kazakh sibirica-ribotypes (3 single-nucleotide substitutions) indicated significant inter-population differences and taxonomic heterogeneity of N. sibirica. Most likely, the processes of homogenization of nuclear ribosomal DNA of N. sibirica samples, the origin of which is associated with hybridization and speciation, are currently continuing.

This overview substantiates the possibility and expediency of blackberry breeding in Central Russia, where it is in demand, but not widespread in horticulture. Significant achievements of world breeding, which gave modern cultivars a large set of economically important qualities and growing interest in it all over the world, including Russian gardeners, make it relevant to work with blackberries as an object of selection, and as a promising garden plant. However, insufficient frost and winter hardiness of the bulk of the cultivars of this culture cause certain difficulties when growing it in the areas with cold winters to which the Central zone of Russia belongs. The expansion of the market of berry products also imposes increasingly high requirements on the complex of economic indicators of new cultivars, primarily the quality of blackberry fruit. In this regard, improving the existing range of varieties of the culture, increasing its adaptive properties and commodity qualities of berries are urgent tasks for breeders when creating new cultivars. The relevance of blackberry breeding is also dictated by the fact that in Russia its domestic range of varieties is represented by only one modern cultivar obtained in the southern region and adapted, first of all, to it. For the Central zone of the country, the cultivars of this plant have not been developed (except for the limited experiments of I.V. Michurin conducted almost 100 years ago). Therefore, the breeding of adapted cultivars of the culture in the climatic conditions of this region may be promising. It is also possible to grow here (with shelter for the winter) the cultivars already created abroad that can give with the right agricultural technology a good industrial harvest, which is confirmed by the practice of amateur and farm gardening, as well as scientific research. The purpose of this work is to designate the leading directions of blackberry breeding, the most important in the conditions of Central Russia and to show prospects of the development of new cultivars of this valuable culture in the specified climatic zone. The analysis of world trends and experience in the blackberry breeding and variety study, as well as the results of our own research of the culture conducted in the Orel region, allow us to consider it promising and relevant to work on improving the range of varieties of this plant in Central Russia. All priority areas of blackberry breeding, indicated in foreign and domestic breeding programs (winter hardiness, high quality of fresh and processed fruit, the correct shape of berries, their large size, the necessary values of biochemical composition, high productivity of plants, thornless shoots and high resistance to diseases and pests), are relevant for this region of our country, while high winter hardiness is currently the most important of them.

Grain with high contents of yellow pigments will add the natural bright-yellow colour to the paste, which unlike a paste with a high level of whiteness, are preferred by consumers. The provitamin activity (vitamin A) and antioxidant activity of the carotenoid pigment increase the biological and nutritional value of the grain with high contents of these pigments. The purpose of this review is to summarize modern knowledge about the biosynthesis and genetic control of pigment accumulation in durum wheat and to assess the main results of research and selection over the past 20 years abroad and in Russia. The trait “concentration carotenoid pigment in grain” (Ypc) is quantitative. However, the prevalence of strong additive gene effects and high heritability have contributed to significant progress in breeding for this trait. Molecular labeling of quantitative trait loci (QTL) that control the synthesis of the carotenoid pigment and the yellowness index (YI) found that they are distributed across all chromosomes of the durum wheat genome. The main QTLs, which determine 60 % of the variation of the trait, were mapped to 7AL and 7BL chromosome. The contribution of these QTLs is associated with allelic variations that control the activity of phytoene synthase (PSY). QTLs with minor effects found on the remaining chromosomes are also reliably mapped using molecular markers. As confirmed in a number of experiments, most of them are QTLs located on 3AS (linked to the LCYE (lycopene ε-cyclase) allele and on 4BS (the LpxB1.1c gene). It has been shown that the LpxB1.1c allele contributes to a decrease in the activity of lipoxygenase, which oxidases carotenoids during the production of end products. This review considered and discusses the problems of molecular markers in breeding programs to increase the concentration of pigments in the grain and improve the color characteristics of the paste.

It has long been known that defects in the structure of the mitochondrial genome can cause various neuromuscular and neurodegenerative diseases. Nevertheless, at present there is no effective method for treating mitochondrial diseases. The major problem with the treatment of such diseases is associated with mitochondrial DNA (mtDNA) heteroplasmy. It means that due to a high copy number of the mitochondrial genome, mutant copies of mtDNA coexist with wild-type molecules in the same organelle. The clinical symptoms of mitochondrial diseases and the degree of their manifestation directly depend on the number of mutant mtDNA molecules in the cell. The possible way to reduce adverse effects of the mutation is by shifting the level of heteroplasmy towards the wild-type mtDNA molecules. Using this idea, several gene therapeutic approaches based on TALE and ZF nucleases have been developed for this purpose. However, the construction of protein domains of such systems is rather long and laborious process. Meanwhile, the CRISPR/Cas9 system is fundamentally different from protein systems in that it is easy to use, highly efficiency and has a different mechanism of action. All the characteristics and capabilities of the CRISPR/Cas9 system make it a promising tool in mitochondrial genetic engineering. In this article, we demonstrate for the first time that the modification of gRNA by integration of specific mitochondrial import determinants in the gRNA scaffold does not affect the activity of the gRNA/Cas9 complex in vitro.

Application of microdissected DNA libraries and DNA probes in numerous and various modern molecular cytogenetic studies showed them as an efficient and reliable tool in the analysis of chromosome reorganization during karyotypic evolution and in the diagnosis of human chromosome pathology. An important advantage of DNA probe generation by metaphase chromosome microdissection followed by sequence-independent polymerase chain reaction in comparison with the method of DNA probe generation using chromosome sorting is the possibility of DNA probe preparation from chromosomes of an individual sample without cell line establishment for the production of a large number of metaphase chromosomes. One of the main requirements for successful application of this technique is a possibility for identification of the chromosome of interest during its dissection and collection of its material from metaphase plates spread on the coverslip. In the present study, we developed and applied a technique for generation of microdissected DNA probes in the case when chromosome identification during microdissection appeared to be impossible. The technique was used for generation of two sets of Whole Chromosome Paints (WCPs) from all chromosomes of two species of free-living flatworms in the genus Macrostomum, M. mirumnovem and M. cliftonensis. The single-copy chromosome technique including separate collection of all chromosomes from one metaphase plate allowed us to generate WCPs that painted specifically the original chromosome by Chromosome In Situ Suppression Hybridization (CISS-Hybridization). CISS-Hybridization allowed identifying the original chromosome(s) used for DNA probe generation. Pooled WCPs derived from homologous chromosomes increased the intensity and specificity of chromosome painting provided by CISS-Hybridization. In the result, the obtained DNA probes appeared to be good enough for application in our studies devoted to analysis of karyotypic evolution in the genus Macrostomum and for analysis of chromosome rearrangements among the worms of laboratory cultures of M. mirumnovem.

Cell migration is an important morphogenetic process necessary at different stages of individual development and body functioning. The initiation and maintenance of the cell movement state requires the activation of many factors involved in the regulation of transcription, signal transduction, adhesive interactions, modulation of membranes and the cytoskeleton. However, cell movement depends on the status of both migrating and surrounding cells, interacting with each other during movement. The surrounding cells or cell matrix not only form a substrate for movement, but can also participate in the spatio-temporal regulation of the migration. At present, there is no exact understanding of the genetic mechanisms of this regulation. To determine the role of the cell environment in the regulation of individual cell migration, we studied the migration of primordial germline cells (PGC) during early embryogenesis in Drosophila melanogaster. Normally, PGC are formed at the 3rd stage of embryogenesis at the posterior pole of the embryo. During gastrulation (stages 6–7), PGC as a consolidated cell group passively transfers into the midgut primordium. Further, PGC are individualized, acquire an amoeboid form, and actively move through the midgut epithelium and migrate to the 5–6 abdominal segment of the embryo, where they form paired embryonic gonads. We screened for genes expressed in the epithelium surrounding PGC during early embryogenesis and affecting their migration. We identified the myc, Hph, stat92E, Tre-1, and hop genes, whose RNA interference leads to premature active PGC migration at stages 4–7 of embryogenesis. These genes can be divided into two groups: 1) modulators of JAK/STAT pathway activity inducing PGC migration (stat92E, Tre-1, hop), and 2) myc and Hph involved in epithelial morphogenesis and polarization, i.e. modifying the permeability of the epithelial barrier. Since a depletion of each of these gene products resulted in premature PGC migration, we can conclude that, normally, the somatic environment negatively regulates PGC migration during early Drosophila embryogenesis.

There are evidences that obese women exhibit a detrimental oocyte quality. However, it remains unclear how this change is associated with obesity, indirectly – or directly through a change in the content and/or composition of lipids in oocytes. The aim of this work was to study effects of a high-fat diet applied to female donor mice on the amount and qualitative composition of lipids of immature and in vivo matured oocytes. A high-fat diet caused larger body weight in female mice compared with the control (p < 0.001; 44.77±1.46 and 35.22±1.57, respectively), and increased the blood levels of cholesterol (p < 0.05; 2.06±0.10 and 1.78±0.10, respectively) and triglycerides (p < 0.05; 2.13±0.23 and 1.49±0.21, respectively). At the same time, this diet does not affect the level of unsaturation of lipids in immature (0.207±0.004 in the experiment and 0.206±0.002 in the control) and matured oocytes (0.212±0.005 in the experiment and 0.211±0.003 in the control). Total lipid content increased during in vivo maturation of mouse oocytes. The amount of lipids was greater in mature oocytes in the experimental group compared to the control (p < 0.01; 8.15±0.37 and 5.83±0.14, respectively). An increase in intracellular lipid amount during oocyte maturation was revealed both after a standard diet (p < 0.05; 4.72±0.48 and 5.83±0.14, respectively) and after a fat-rich diet (p < 0.001; 3.45±0.62 and 8.15±0.37, respectively). Thus, during in vivo oocyte maturation in mice the content of intracellular lipids enhanced, the high-fat diet aggravated this dynamics of lipid increase during in vivo maturation of oocytes.

This is a review of studies on the genetic polymorphism of modern and ancient populations of the north of Asia and America, with the aim of reconstructing the history of migrations of ancient marine hunters in the Okhotsk Sea region. The data on mitochondrial DNA polymorphism and the “Arctic” mutation distribution – the rs80356779-A variant of the CPT1A gene – were analyzed. It is known that the “Arctic” variant of the CPT1A gene is widely distributed in modern populations of the Eskimos, Chukchis, Koryaks, and other peoples of the Okhotsk Sea region, whose economic structure is associated with marine hunting. According to paleogenomic data, the earliest cases of the “Arctic” variant of the CPT1A gene were found in the Greenland and Canadian Paleoeskimos (4 thousand years ago), among representatives of the Tokarev culture of the Northern Priokhotye (3 thousand years ago), and among the bearers of the culture of the late Jomon of Hokkaido (3.5–3.8 thousand years ago). The results of the analysis revealed several migration events associated with the spread of marine hunters in the Okhotsk Sea region. The latest migration, which left traces on bearers of the Epi-Jomon culture (2.0–2.5 thousand years ago), introduced the mitochondrial haplogroup G1b and the “Arctic” variant of the CPT1A gene from the north of Priokhotye to Hokkaido and neighboring territories of the Amur Region. Traces of earlier migration, which also brought the “Arctic” mutation, were recorded in the Hokkaido population of the late Jomon period (3.5–3.8 thousand years ago). A phylogenetic analysis of mitochondrial genomes belonging to the rare haplogroup C1a, found in populations of the Far East and Japan, but phylogenetically related to the C1-haplogroups of the Amerindians, was carried out. The results of the analysis showed that the divergence of mitochondrial lineages within the C1a haplogroup occurred in the range from 7.9 to 6.6 thousand years ago, and the age of the Japanese branch of the C1a haplogroup is approximately 5.2 thousand years. It is not yet known whether this migration is associated with the spread of the “Arctic” variant of the CPT1A gene or the presence of C1a haplotypes in the population of the Japanese islands marks another, earlier, episode of the migration history linking the populations of Northwest Pacific and North America.