Resistance mechanisms involved in complex immunity of wheat against rust diseases

The review is devoted to the disclosure of the modern concept of plant immunity as a hierarchical system of plant host protection, controlled by combinations of major and minor resistance genes (loci). The “zigzag” model is described in detail for discussing the molecular bases of plant immunity with key concepts: pathogen-associated molecular patterns triggering innate immunity, ambivalent effectors causing susceptibility, but when interacting with resistance genes, a hypersensitive reaction or alternative defense mechanisms. There are three types of resistance in cereals: (1) basal resistance provided by plasma membrane-localized receptors proteins; (2) racespecific resistance provided by intracellular immune R-receptors; (3) partial resistance conferred by quantitative gene loci. The system ‘wheat (Triticum aestivum) – the fungus causing leaf rust (Puccinia triticina)’ is an interesting model for observing all the resistance mechanisms listed above, since the strategy of this pathogen is aimed at the constitutive use of host resources. The review focuses on known wheat genes responsible for various types of resistance to leaf rust: race-specific genes Lr1, Lr10, Lr19, and Lr21; adult resistance genes which are hypersensitive Lr12, Lr13, Lr22a, Lr22b, Lr35, Lr48, and Lr49; nonhypersensitive genes conferring partial resistance Lr34, Lr46, Lr67, and Lr77. The involvement of some wheat R-genes in pre-haustorial resistance to leaf rust has been discovered recently: Lr1, Lr3a, Lr9, LrB, Lr19, Lr21, Lr38. The presence of these genes in the genotype ensures the interruption of early pathogenesis through the following mechanisms: disorientation and branching of the germ tube; formation of aberrant fungal penetration structures (appressorium, substomatal vesicle); accumulation of callose in mesophyll cell walls. Breeding for immunity is accelerated by implementation of data on various mechanisms of wheat resistance to rust diseases, which are summarized in this review

Challenges and prospects for developing genetic resistance in common wheat against stem rust in Western Siberia

Current studies on bread wheat resistance to stem rust have two main subjects: complex analysis for resistance of bread wheat germplasm using molecular markers, field screening and laboratory tests against samples of different fungal populations, and searching for sources and donors of new genes and gene loci, including cultivated and wild relatives of wheat. To achieve adequate genetic control of the disease, an integral approach is important, incorporating both data on sources of resistance and relevant information on pathogenic populations existing in the region, their race composition and dynamics of virulence genes. The analysis of experimental data on field screening of bread wheat varieties from the CIMMYT nursery germplasm for stem rust resistance in the Omsk and Novosibirsk regions, together with laboratory testing of infection samples on the international set of wheat differential lines, suggests that a separate “Asian” population of Puccinia graminis f. sp. tritici exists in Western Siberia and the Altai Territory. Wheat resistance genes Sr2, Sr6Ai#2, Sr24, Sr25, Sr26, Sr31, Sr39, Sr40, Sr44, and Sr57 are of practical interest for advanced wheat breeding programs for stem rust immunity in Western Siberia. This review provides an analysis of the gene sources that remain effective against the West Siberian population of P. graminis, in order to facilitate the initial stage of selection of breeding material to develop a stable genotype by gene pyramiding. The basic requirements for conducting a phytopathological test of breeding material are presented. A list of molecular markers for the mentioned resistance genes, both widely used in marker-assisted selection and requiring verification, has been compiled

Methodical approaches to identification of effective wheat genes providing broad-spectrum resistance against fungal diseases

Among the pathogenic complex of the common wheat there is a causal agent of leaf and stem diseases: (rusts and powdery mildew), which has economic importan ce for most of the Russian regions. We propose a methodological approach for confirmation of effec tiveness of wheat genes conferring broad-spectrum resistance to different types of fungal diseases, which integrates traditional field tests and current genotyping techniques with molecular DNA markers. The pro posed approach includes the following steps: 1) evaluating of wheat genotypes using molecular DNA markers; 2) field tests for genotypes; 3) confirma tion of effective ness of broad-spectrum resistance genes by matching field scores and data from mole cular markers. A protocol has been proposed for geno typing varieties and wheat lines using markers linked to Lr16/Sr23, Lr24/  Sr24, Lr19/ Sr25, Lr26/Sr31/Yr9/Pm8, Lr37/Sr38/Yr17 and the gene Lr34(=Sr57/Yr18/Pm38) with a pleiotropic effect. Markers to the genes Lr6Ai#2/Sr6Ai#2/Pm6Ai#2 transferred from Thinopyrum intermedium into the genomes of Russian wheat varieties and markers to a new translocation from Aegi lops spel toides with a group of genes, designated as LrAsp7/SrAsp7/PmAsp7, were tested. When evaluating the contribution of the genes (including genes located on the alien translocations) to the formation of common wheat resistance to fungal diseases, it is necessary to use an extended sample, including genotypes carrying the same group of genes in a different genetic background. In addition, recommendations are given on the terms and frequency of monitoring of fungal diseases in Western Siberia, depending on the pathogen. The methodological approach proposed in the article can be used for identification and evaluation of the efficacy of the genes determining protection of wheat from fungal diseases. This approach is applicable in the investigation of genetic collections consisting of isogenic lines, sources and donors of resistance genes, as well as in the development of wheat genotypes using marker-assisted selection

A system approach to the modeling of fungal infections of the wheat leaf

Currently, studies on the mechanisms of the pathogenesis of plant diseases and their distribution in crops are intensively conducted in Russia and the world. First of all, this interest is associated with a significant effect of pathogens on the harvest. In Western Siberia, brown rust and powdery mildew are almost annually recorded in the crops of spring and winter wheat, reaching in some years up to the epiphytotic level. In this regard, methods for monitoring the condition of crops in order to predict their dynamics and plan agrotechnological events to control the state of plants in crops, including the development of fungal infection are developing. Models of fungal infections development on the wheat leaf (for example, brown rust) are used to monitor, predict and control the state of crops in order to optimize the growing process. Mathematical models allow computational experiments to make predictions about the risk dynamics of infections in different scenarios of global weather changes. Such designation of models assumes their hierarchical structure characteristic of multilevel modeling systems. This review presents models for the development of foliar fungal infections in crops, and formulates the methodological aspects of system modeling that can be used for adapting existing models and their units, and developing new models based on them. The article presents the structure of the hierarchical system for modeling the development of leafy infection, provides an overview of the units constituting the system, and discusses the issues of parametric adaptation of submodels. We demonstrated that, to date, plant growth and development models have been developed with varying degrees of detail. Currently, to develop a system for modeling the development of an infection in a crop, it is necessary to determine a large body of available experimental data and, by taking into account this data, we can put together a model as a system consisting of model modules, for which the models of basic processes have already been developed and described

Species identification of spider mites (Tetranychidae: Tetranychinae): a review of methods

Spider mites (Acari: Tetranychidae) are dangerous pests of agricultural and ornamental crops, the most economically significant of them belonging to the genera Tetranychus, Eutetranychus, Oligonychus and Panonychus. The expansion of the distribution areas, the increased harmfulness and dangerous status of certain species in the family Tetranychidae and their invasion of new regions pose a serious threat to the phytosanitary status of agroand biocenoses. Various approaches to acarofauna species diagnosis determine a rather diverse range of currently existing methods generally described in this review. Identification of spider mites by morphological traits, which is currently considered the main method, is complicated due to the complexity of preparing biomaterials for diagnosis and a limited number of diagnostic signs. In this regard, biochemical and molecular genetic methods such as allozyme analysis, DNA barcoding, restriction fragment length polymorphism (PCR-RFLP), selection of species-specific primers and real-time PCR are becoming important. In the review, close attention is paid to the successful use of these methods for species discrimination in the mites of the subfamily Tetranychinae. For some species, e. g., the two-spotted spider mite (Tetranychus urticae), a range of identification methods has been developed – from allozyme analysis to loop isothermal amplification (LAMP), while for many other species a much smaller variety of approaches is available. The greatest accuracy in the identification of spider mites can be achieved using a combination of several methods, e. g., examination of morphological features and one of the molecular approaches (DNA barcoding, PCR-RFLP, etc.). This review may be useful to specialists who are in search of an effective system for spider mite species identification as well as when developing new test systems relevant to specific plant crops or a specific region

The gene Sr38 for bread wheat breeding in Western Siberia

Present-day wheat breeding for immunity exploits extensively closely related species from the family Triticeae as gene donors. The 2NS/2AS translocation has been introduced into the genome of the cultivated cereal Triticum aestivum from the wild relative T. ventricosum. It contains the Lr37, Yr17, and Sr38 genes, which support seedling resistance to the pathogens Puccinia triticina Eriks., P. striiformis West. f. sp. tritici, and P. graminis Pers. f. sp. tritici Eriks. & E. Henn, which cause brown, yellow, and stem rust of wheat, respectively. This translocation is present in the varieties Trident, Madsen, and Rendezvous grown worldwide and in the Russian varieties Morozko, Svarog, Graf, Marquis, and Homer bred in southern regions. However, the Sr38 gene has not yet been introduced into commercial varieties in West Siberia; thus, it remains of practical importance for breeding in areas where populations of P. graminis f. sp. tritici are represented by avirulent clones. The main goal of this work was to analyze the frequency of clones (a)virulent to the Sr38 gene in an extended West Siberian collection of stem rust agent isolates. In 2019–2020, 139 single pustule isolates of P. graminis f. sp. tritici were obtained on seedlings of the standard susceptible cultivar Khakasskaya in an environmentally controlled laboratory (Institute of Cytology and Genetics SB RAS) from samples of urediniospores collected on commercial and experimental bread wheat fields in the Novosibirsk, Omsk, Altai, and Krasnoyarsk regions. By inoculating test wheat genotypes carrying Sr38 (VPM1 and Trident), variations in the purity of (a)virulent clones were detected in geographical samples of P. graminis f. sp. tritici. In general, clones avirulent to Sr38 constitute 60 % of the West Siberian fungus population, whereas not a single virulent isolate was detected in the Krasnoyarsk collection. The Russian breeding material was screened for sources of the stem rust resistance gene by using molecular markers specific to the 2NS/2AS translocation. A collection of hybrid lines and varieties of bread spring wheat adapted to West Siberia (Omsk SAU) was analyzed to identify accessions promising for the region. The presence of the gene was postulated by genotyping with specific primers (VENTRIUP-LN2) and phytopathological tests with avirulent clones of the fungus. Dominant Sr38 alleles were identified in Lutescens 12-18, Lutescens 81-17, Lutescens 66-16, Erythrospermum 79/07, 9-31, and 8-26. On the grounds of the composition of the West Siberian P. graminis f. sp. tritici population, the Sr38 gene can be considered a candidate for pyramiding genotypes promising for the Novosibirsk, Altai, and Krasnoyarsk regions

Raise and characterization of a bread wheat hybrid line (Tulaykovskaya 10 × Saratovskaya 29) with chromosome 6Agi2 introgressed from Thinopyrum intermedium

Wheatgrass Thinopyrum intermedium is a source of agronomically valuable traits for common wheat. Partial wheat–wheatgrass amphidiploids and lines with wheatgrass chromosome substitutions are extensively used as intermediates in breeding programs. Line Agis 1 (6Agi2/6D) is present in the cultivar Tulaykovskaya 10 pedigree. Wheatgrass chromosome 6Agi2 carries multiple resistance to fungal diseases in various ecogeographical zones. In  this work, we studied the transfer of chromosome 6Agi2 in hybrid populations Saratovskaya 29×Tulaykovskaya 10 (S29×T10) and Tulaykovskaya 10×Saratovskaya 29 (T10×S29). Chromosome 6Agi2 was identified by PCR with chromosome-specific primers and by genomic in situ hybridization (GISH). According to molecular data, 6Agi2 was transmitted to nearly half of the plants tested in the F2 and F3 generations. A new breeding line 49-14 (2n = 42) with chromosome pair 6Agi2 was isolated and characterized in T10×S29 F5 by GISH. According to the results of our field experiment in 2020, the line had high productivity traits. The grain weights per plant (10.04±0.93 g) and the number of grains per plant (259.36±22.49) did not differ significantly from the parent varieties. The number of grains per spikelet in the main spike was significantly higher than in S29 (p ≤ 0.001) or T10 (p ≤ 0.05). Plants were characterized by the ability to set 3.77±0.1 grains per spikelet, and this trait varied among individuals from 2.93 to 4.62. The grain protein content was 17.91 %, and the gluten content, 40.55 %. According to the screening for fungal disease resistance carried out in the field in 2018 and 2020, chromosome 6Agi2 makes plants retain immunity to the West Siberian population of brown rust and to dominant races of stem rust. It also provides medium resistant and medium susceptible types of response to yellow rust. The possibility of using lines/varieties of bread wheat with wheatgrass chromosomes 6Agi2 in breeding in order to increase protein content in the grain, to confer resistance to leaf diseases on plants and to create multiflowered forms is discussed

Stem rust in Western Siberia – race composition and effective resistance genes

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

Прямые и косвенные методы определения нуклеотидного состава ДНК последовательностей микроорганизмов

Typing of bacterial populations and identification of microorganisms are the overriding priorities in the field of prophylaxis, diagnosis and treatment of bacterial infections. Over the recent two decades rapidly developing approaches to molecular typing of bacterial populations have become an essential tool for the mentioned task. The information encoded in nucleic acids is more complete as compared to other characteristics of an organism. It can be obtained by either direct determination of genome sequences or by using a variety of techniques, that allow to indirectly assess the nucleotide composition in a representative genome locus of a microorganism under study. The article provides an overview of the literature data on direct and indirect methods of determining nucleotide composition of DNA sequences in microorganisms (multiple locus sequence typing, multiple sequeneed sites typing, denaturing gel electrophoresis, high-sensitivity melting curve analysis, DNA macro(micro)arrays).Типирование бактериальных линий и идентификация микроорганизмов - чрезвычайно важные задачи в области профилактики, диагностики и лечения бактериальных инфекций. За последние два десятилетия бурно развивающиеся молекулярные подходы к типированию бактериальных линий стали необходимым инструментом для решения этой задачи. Информация, которую могут дать нуклеиновые кислоты, является наиболее полной по сравнению с другими характеристиками организма. Получить ее можно как непосредственным определением избранных последовательностей генома, так и с помощью различных техник, позволяющих, косвенно оценить нуклеотидный состав репрезентативного участка генома исследуемого микроорагнизма. Статья посвящена обзору литературных данных по прямым и косвенным методам определения нуклеотидного состава ДНК последовательностей микроорганизмов (типирование по мультилокусным сик-венсам, типирование по множеству отсеквенированных участков, электрофорез в денатурирующей системе, высокочувствительный анализ кривых плавления, ДНК макро(микро)чипы)

Direct and indirect methods of determining DNA nucleotide sequences in microorganisms

Typing of bacterial populations and identification of microorganisms are the overriding priorities in the field of prophylaxis, diagnosis and treatment of bacterial infections. Over the recent two decades rapidly developing approaches to molecular typing of bacterial populations have become an essential tool for the mentioned task. The information encoded in nucleic acids is more complete as compared to other characteristics of an organism. It can be obtained by either direct determination of genome sequences or by using a variety of techniques, that allow to indirectly assess the nucleotide composition in a representative genome locus of a microorganism under study. The article provides an overview of the literature data on direct and indirect methods of determining nucleotide composition of DNA sequences in microorganisms (multiple locus sequence typing, multiple sequeneed sites typing, denaturing gel electrophoresis, high-sensitivity melting curve analysis, DNA macro(micro)arrays)