Nowadays, the world’s largest Potato Genebanks, including VIR Potato Genebank, hold about 98 thousand accessions of potato and its wild relatives. This gene pool, which has been accumulated for almost a century, represents a huge genetic diversity of tuber bearing species of the genus Solanum L., which has a great importance for basic and applied research in general, and for human food security. The genebanks of potato and other crops have three highly important tasks such as permanent replenishment of collection material, ensuring its preservation by various storage and maintaining methods, including seed and vegetative propagation, its all-round use in basic and applied research, as well as the improvement of the efficiency of agricultural production. Analysis of performance of the above tasks in genebanks and research institutes in most countries concerned with storage, study and use of potato germplasm, shows great results and achievements, both in terms of its biology and its improvement as a food crop. However, the above three ways to perform tasks still need to be improved in connection with progress made over past decades, in particular in the field of basic and applied sciences. In this paper, a brief analysis of the status of conservation, study and use of potato genetic resources and its wild relatives in the domestic and foreign breeding, as well as solutions of problems in these areas are provided. A great leap forward today is the use of molecular genetic methods for genotyping collection material in gene banks to identify and itemize collection samples, as well as for using this material in basic and applied research, including breeding programs. Coordination of efforts for the collection of wild species that are not in the collections or are represented by a small number of samples, as well as the exchange of material and information about it, will help expand genetic diversity in genebanks and knowledge of the biological features of the potato.

The common potato Solanum tuberosum is the fourth most important crop in the world and like many other cultivated plants is characterized by low level of genetic diversity. The most effective approach to broaden genetic diversity of breeding varieties is based on the introgression of genetic material of wild and cultivated species belonging to section Petota Dumort. of the genus Solanum L. This section, according to estimates by different taxonomists, includes from 112 to 235 species. At the same time, because of the barriers of prezygotic and postzygotic incompatibility, only about 10 % of wild potato species have been actively involved into the breeding process and their genetic material has been introgressed into the gene pool of varieties. To date, molecular genetics, genomics, and biotechnology have accumulated a large amount of information, allowing the problems of extension of the genetic diversity of common potato to be addressed. The article presents a review of modern data about the genetic factors determining prezygotic and postzygotic incompatibility, about the features of involvement in the hybridization process of the self-compatible and self-incompatible species of section Petota and species with different values of the endosperm balance number (EBN), as well as possible mechanisms of interaction between the parental genomes during the formation of the endosperm of the hybrid seed. Data are provided on the value of the theory of EBN for the further development of applied research aimed at increasing the genetic diversity of the breeding gene pool. This review discusses the traditional and modern approaches and methods of overcoming interspecific incompatibility and gives examples of successful studies on introgressive hybridization of potato. The article is preceded by information about the genetic diversity of potato species belonging to section Petota of the genus Solanum.

Interspecific hybridization is the primary method of potato breeding for resistance to pathogens. By introgressing genetic material from various species of the genus Solanum L. and selecting the best combinations, it is possible to merge, in a single genotype, both high productivity and resistance to diseases and pests. Among the most impressing outcomes of potato breeding, we find varieties resistant to late blight, potato virus Y and nematodes. In the pedigrees of many recent varieties (breeding lines) that are resistant to pathogens of different nature (fungi, oomycetes, bacteria or viruses), we find genetic material of Solanum andigenum, S. demissum, S. stoloniferum, S. acaule, S. vernei and other wild and cultivated potato species. The breeding value of tuber-bearing Solanum species depends on their compatibility with the cultivated potato and the mechanism of target trait inheritance. To overcome incompatibility in crosses, breeders employ ploidy manipulation in the parental forms, bridge crosses, the mediator method and various in vitro technologies. Potato genotypic variation is significantly expanded by interspecific hybridization of wild and cultivated potato relatives. The main components of breeding technology based on interspecific potato hybrids are the identification of promising initial genotypes, the control over the introgression of the target traits through the crosses, the selection of hybrid clones prospective for practical breeding and the assessment of their donor properties. All of these processes are greatly accelerated and promoted by the methods of marker-assisted selection. Advanced lines and clones developed by interspecific hybridization manifest a high diversity of genotypes and particular genes and are unique donors for breeding new varieties maintaining high and durable resistance to diseases and pests.

The casual agent of potato wart Synchytrium endobioticum (Schilb.) Perc. and potato golden nematode (PGN) Globodera rostochiensis (Wollenweber) Behrens are the quarantine species causing the most widespread and destructive diseases of potato in the Russian Federation and other countries of the world. The potato pale nematode Globodera pallida (Stone) Behrens is not found in Russia, although in the European Union it is found everywhere. The review provides information on the harmfulness of S. endobioticum and PGN. To date, 43 pathotypes of S. endobioticum and 5 pathotypes of PGN have been revealed in the world. In the Russian Federation, only the first (D1) pathotype of potato wart and pathotype Ro1 of PGN have been found. Modern sets of differentials for S. endobioticum and PGN and methods of pathotype composition determination, including efforts to develop molecular markers (SSR) to determine the race of S. endobioticum, are presented. Data on the resistance of commercial potato cultivars to these quarantine diseases and methods for resistance determination are reviewed. Modern data on the genetics of potato resistance to S. endobioticum, G. rostochiensis and G. pallida, including mapping and cloning of R-genes, are presented. Available literature data on molecular markers of R-genes for marker assisted selection and the evaluation of their effectiveness are presented. The use of multiplex systems allows the presence of several genes for resistance to one or more pathogens to be analyzed at once. Mechanisms of potato quantitative resistance to S. endobioticum and PGN and adaptation processes in pathogens populations resulting in overcoming resistance of host are discussed. Cultivation of cultivars poorly susceptible to PGN can stimulate the adaptive variability of the pathogen and induce virulent pathotypes for 2–3 pathogen generations.

The potato (Solanum tuberosum), one of the most important food crops in the world, is infected by various viruses, nine of which have great economic significance, causing substantial losses in the yield and quality of the crop. To minimize consequences of virus infections, in developed countries specific phytosanitary measures have been established and are being improved to monitor the spread of viruses and certify seed potato material using virus diagnostics and production of virus-free potato cultivars. However, in the longer-term, the development and deployment of potato cultivars resistant to viruses would be a priority. Some new potato cultivars and lines resistant to many viruses have already been generated using either traditional breeding methods or genetic engineering. For this purpose, natural resistance genes, primarily from wild Solanum species, or virus derived nucleotide sequences have been used as sources of resistance. However, these approaches have essential limitations because the acquired resistance is highly specific (against individual viruses only), is not durable, can be overcome by viruses and, finally due to regulatory bans on genetically modified organisms. Recently developed new genome editing technologies with the potential to be a powerful tool for gene design open up broad opportunities for development of next-generation resistance genes. The most promising approaches are (1) site-directed mutagenesis of the genes conferring specific resistance to make their action much broader and (2) the use of non-specific (nonhost) resistance to generate plants resistant to unrelated viruses and, in some cases, to other pathogens and even abiotic stresses. Identification of genes involved in mechanisms of non-host resistance is just beginning. The cell nucleus is a new source of novel factors involved in various signaling pathways resulting in defence response to virus infection. This review focuses on the approaches and challenges related to the development of potato plants resistant to virus infections.

The problem of aphid resistance of potato genetic resources is discussed. Generally, resistance to the green peach aphid (Myzus persicae Sulzer) and the potato aphid (Macrosiphum euphorbiae Thomas) is analyzed in all available literature sources. The Solanum tuberosum L. gene pool contains very few resistant forms. Accessions highly resistant to M. persicae were revealed among 36 of 86 examined wild potato species. The largest number of resistant forms was found among S. bulbocastanum Dun., S. tarijense Hawkes, S. infundibuliforme Phil., S. canasense Hawkes and S. stoloniferum Schlechtd. et Bché. The forms highly resistant to M. euphorbiae belong to 24 of 85 studied species, namely to 10 of 18 series; the species S. bulbocastanum, S. stoloniferum and S. demissum Lindl. include the maximum number of resistant forms. Wild species accessions with specific and group resistance to aphids were revealed. Glandular pubescence of leaves and stems in such species as S. polyadenium Greenm., S. tarijense and S. berthaultii Hawkes is considered as the main mechanism of resistance. Hybrids between S. tuberosum and S. berthaultii were widely used in breeding programs; however, the presence of glandular trichomes was linked to a number of undesirable characters. It is expected that association between the trichome conditioned insect resistance of S. berthaultii and undesirable agronomic traits could be overcome with the use of molecular genetic methods. Studies of the antifeedant activity of potato glycoalkaloids and their aglucons produced controversial results. In numerous works the aphid resistance of potato is connected with plant physiological state. Differences among wild potato accessions in the localization of resistance factors (leaf surface, epidermis, mesophyll, floema) were found that were indicative of differences of resistance mechanisms in the studied forms. Works on investigating induced aphid resistance in potato have great theoretical and practical significance.

There is a set of wild potato species valuable for breeding, in particular 1 EBN diploid species from Mexico, which is practically not crossable to cultivated potatoes, including Solanum tuberosum dihaploids (2х, 2 EBN), because of strict pre- and postzygotic interspecific reproductive barriers. It is proposed to involve that species germplasm into breeding by using the original SvSv-lines (F2 S. tuberosum dihaploids×S. verrucosum), in which St -alleles have been substituted for Sv from the self-compatible diploid species S. verrucosum not producing stylar S-RNase. It was anticipated that SvSv-lines have the same ability for elimination of prezygotic incompatibility in interspecific hybridization as S. verrucosum due to S-genes of that species in homozygous state. However, their use would help avoid undesirable effects associated with S. verrucosum application (male sterility and reduced tuber formation in hybrids). The aim of the research was estimation of the efficiency of using SvSv-lines, in comparison with S. verrucosum, as a bridge for involvement of the 1 EBN potato species S. bulbocastanum, S. pinnatisectum and S. polyadenium into breeding. It was revealed that SvSv-lines excels S. verrucosum in hybridization efficacy due to abundant and prolonged flowering in later term than S. verrucosum, when flowering of pollinator species occurs. There were significantly less sterile or low fertility genotypes among the hybrids between SvSv-lines and 1 EBN wild species. They had higher ability for tuber formation, and so they were suitable for long term field trials, contrast to hybrids with S. verrucosum. The interspecific hybrids produced were crossed as female parents to S. tuberosum dihaploids.

Increasing interest to cytoplasmic male sterility (CMS) and searching for restoration of pollen fertility (Rf) genes in potato is determined by a new way in the modern breeding of this important crop, the development of heterotic hybrids obtained after crosses of inbred diploid lines. The paper reviews the main results of studies on CMS-Rf genetic systems in different species of cultivated plants, the modern methods and approaches of investigating molecular mechanisms of CMS and pollen fertility restoration, and also the available literature data on the status of these studies in potato. The nature of chimeric mitochondrial genes accounting for cytoplasmic male sterility is considered; the peculiarities of the structure and functions of restoration of pollen fertility genes are discussed; examples of CMS-Rf genetic systems in cultivated plant species including representatives of the family Solanaceae are presented. The main results of research on molecular mechanisms of CMS and fertility restoration obtained in the post-genomic era for various plant species using methods of transcriptomic and proteomic analyses are provided. As in many plant species, cytoplasmic male sterility in potato is of hybrid origin. The results of investigating genetic control of male sterility in potato are presented that have been carried out using conventional approaches (hybridological analysis) and led to the formation of the concept of genic cytoplasmic male sterility in some species of section Petota of the genus Solanum. The characteristics of potato cytoplasms types which are associated with male sterility are given. According to classification of Hosaka, Sanetomo (2012), these types include: T/beta, W/gamma and D, each distinguished by the phenotypic appearance of male sterility traits and also by the frequency of occurrence in the breeding varieties gene pool and in various potato species. The results of studies on developing DNA markers for identification of various potato cytoplasm types are presented.

In recent years, marker-assisted selection (MAS) has been intensively used to increase potato breeding efficiency. Large-scale studies of the potato genome and genes exploiting next-generation sequence (NGS) approaches are required for broad application of MAS, genomic selection as well as genomic editing (the newest approach for creating potato with desired properties). In this review, trends in potato NGS-based research are overviewed, and related Internet resources are systematized. Special attention is given to peculiarities of the models and the approaches used in potato genetic studies, taking into account the complex organization of its genome and a high level of heterozygosity. In genetic studies diploids are used often, including diploid potato species, artificially obtained heterozygous dihaploids and homozygous double monoploids. The availability of artificially created diploid forms played an essential role in potato genome sequencing, which was completed in 2011. The Potato Genome Sequencing Consortium activities included not only constructing genome libraries, sequencing, assembling and annotation of the genome, but also genome sequence-based investigations uncovering features of potato genome evolution, SNP identification, analysis of genes and gene networks regulating resistance to phytopathogens and technological characteristics. An important outcome of the genome sequencing was further identification of more than 8 thousand SNPs and approbation of the Genotyping-by-sequencing (GBS) method on potato, which is the basis for potato genomic selection and for discovery of economically important genes using genome wide association studies (GWAS). Optimization of existing bioinformatic tools to support these studies, taking into account potato genome organization peculiarities, are carried out. This review gives analysis of databases containing potato genome and transcriptome sequencing results, as well as accompanying resources. This information should prove useful while planning comparative assays of potato transcriptome or application of DNA-markers. Sequencing of the genome as well as transcriptomes and microRNomes of cultivated potato and its wild relatives, on one hand, is of fundamental interest, assisting in detecting features of genome evolution, ontogenetic development and mechanisms of various environmental stresses responses. On the other hand, it is the basis for a wide range of practical applications for developing effective genomic and gene-specific markers and marker-assisted breeding of new potato cultivars with desired properties.

There are several technologies for plant genome editing, of which the most simple and universal is CRISPR/Cas. Currently, this technology is widely used for gene knockout, deleting genome fragments and inserting exogenous sequences in the plant genome. For each of these applications, many different types of genetic tools have been developed that are used by various research groups to solve specific problems. The CRISPR/Cas technology for plant genome editing is at an early stage of optimization, which is reflected by the ongoing search for the most effective, simple and flexible techniques. As a result, experimental work has to be preceded by a rather long and laborious process of selecting a genetic tool that will be optimal for a specific experimental task. In our review we describe the main variants of the CRISPR/Cas technology used to edit a plant genome. We classify them in terms of experimental tasks solved, major components and technology performance. In the first half of the review a detailed description of two major components of CRISPR/Cas technology – nuclease and guide RNA – is given, the effect of structural features of these elements on editing efficiency is analyzed. Experimental data on the relationship between editing efficiency and nucleotide sequence of guide RNA are generalized. We also give the characteristic for different variants of nucleases used for plant genome editing and discuss their benefits for different experimental purposes. In the second half of the review various strategies for expression of CRISPR/Cas elements in plant cells, in particular, advantages and disadvantages of stable transformation and transient expression, are discussed. The effect of various regulatory elements of genes encoding nuclease and guide RNA on editing efficiency is described. Special emphasis is placed on the techniques of increasing targeted gene replacement efficiency.

According to FAO (Food and Agricultural Organization of the United Nation), potato is the fourth crop in terms of food production after rice, wheat and maize, and the first among the tubers and roots. The importance of potato is difficult to overestimate; it is a valuable source of carbohydrates, antioxidants and vitamins. A huge number of investigations are focused on the study of metabolic processes occurring in the potato plant in order to elucidate the mechanisms responsible for productivity and accumulation of compounds that determine taste and nutritional quality, keeping quality of tubers, plant resistance, etc. The sum of metabolites, which is produced as a result of metabolic network activity, is defined as metabolome. Complex studies of metabolic diversity with the use of modern state-of-the-art chromatography approaches and highly precise detection of individual compounds revealed specificity of metabolic spectra from subcellular to organism levels and its amazing plasticity under the influence of a variety of internal and external stimuli. Metabolomic approaches are already in use for phenotyping available species, lines and varieties as well as for evaluation of potato plant resistance to environmental challenges and for detection of changes in tubers during storage. Metabolome profiling is widely employed to study differences between genetically modified forms of potatoes from untransformed relatives. A limited number of systemic studies on potatoes combines metabolome investigation with genome, transcriptome and proteome analysis and suggests an important role of the genome in the determination of metabolic rates. It is obvious that the search for biochemical markers depends on standartization of cultivation techniques, sample preparation and subsequent analysis similar to what has been developed for progress in genomic and transcriptomic studies. In the future, potato metabolome studies might complete classical and molecular approaches to develop new lines and varieties.

Genetic identification of potato varieties is a demanded instrument for development of new cultivars registration system, protection of plant breeders’ rights, and variety homogeneity control. The most perspective approach for distinction and identification of varieties continues to remain the use of short tandem repeats. STR amplification with the subsequent high resolution electrophoresis allows such a unique characteristic of a variety to be obtained as the DNA profile. A large scale of samples requires the creation of a robust and time-saving technique based on fragment sizing. We selected 10 polymorphic STR loci of potato: STI0032, STG0016, STI0001, STI0004, STM1104, STM5127, STI0030, STI0033, STI0014, STM5114 and designed a multiplex panel for potato DNA profiling. Fluorescent labelling of primers and size distinction of amplicones allowed us to use one tube for PCR and capillary electrophoresis. We also modified the CTAB-protocol for DNA extraction from tubers and other parts of potato plants, the PCR mix recipe and the amplification protocol for good results. Using Genetic Analyzer allows the length of alleles to be defined with an accuracy of one nucleotide and digitized genetic profiles to be developed. We created a unique DNA profile for each of 40 varieties and 23 breeding lines from Russia and other countries and evaluated the homogeneity of 8 varieties. The proposed technique оf potato DNA profiling allows a large number of samples to be rapidly analyzed in the 96-well plate format.

Molecular markers have become crucial part of genetics due to their use in various branches of it, such as positional cloning, which includes identification of genes responsible for desired traits and management of backcrossing programs, as well as in modern plant breeding, and human forensics. Retrotransposons are a major component of all eukaryotic genomes, which makes them suited as molecular markers. The retrotransposons comprise most of large genomes among plants; differences in their prevalence explain most of the variation in genome size. These ubiquitous transposable elements are scattered in all of genome and their replicative transposition allows insert itself into a genome without deletion of the original elements. Retrotransposon activity can occur during development, cell differentiation and stress, and a source of chromatin instability and genomic rearrangements. Both the overall structure of retrotransposons and the domains responsible for the various phases of their replication are highly conserved in all eukaryotes. A high proportion of the retroelements have lost their autonomous transposition ability, either by point mutations and/or deletions, many of them seem to embody defective elements with deletions. Various molecular marker systems have been developed that exploit the ubiquitous nature of these genetic elements and their property of stable integration into dispersed chromosomal loci that are polymorphic within species. The utility of LTR-retrotransposon-based markers, not only for genetic analysis and map construction, in addition also for the isolation and characterization of LTR retrotransposons, such as the long terminal repeats or the internal genes they contain. This review encompasses description of the range of retrotransposon-based marker systems established for plants and evaluation of the role of retrotransposon markers in genetic diversity analysis of plant species.

Currently three species are recognized in Russia within the genus Elymus subsection Pendulini, namely, E. pendulinus, E. brachypodioides and E. vernicosus. The degree and quality of lemma and stem node vestitures and ecology are considered important characters for species delineation. In Primorsky krai and Altai Republic we have found a number of mixed populations in which there is visually continuous variation in lemmas vestitures from being completely glabrous to densely puberulent or pilose. Additionally, there are a number of populations in Primorsky krai in which individuals having either smooth or pilous stem nodes grow together. A study of polymorphism of ISSR markers among selective accessions of three species from different locations was carried out together with the reference species E. ciliaris and E. gmelinii. The consensus dendrogramm constructed by results of ISSR markers has shown no taxon specific patterns in accessions of the subsection Pendulini. Hybrids between the individuals of different species of the subsection in six cross combinations have been created. All F1 plants had normally developed open anthers, seed fertility (SF) ranged from 8 % to 89 % in different combinations. In F2 populations no sterile individuals or increase of SF up to normal values were observed. Hence, three taxa form a unified recombination gene pool. The diagnostic characters were found to be controlled by one pair of alternative alleles for glabrous vs. hairy stem nodes, and by one or two pairs of alleles in different cross combinations for glabrous vs. hairy lemmas. These characters can be considered as normal inter- and/or intra-population variation. Therefore, E. brachypodioides and E. vernicosus need to be relegated to infraspecific rank within Elymus pendulinus s. l. as varieties.