Browsing by Author "Kalendar, Ruslan"

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  • Tanhuanpää, Pirjo; Erkkilä, Maria; Kalendar, Ruslan; Schulman, Alan H; Manninen, Outi (BioMed Central, 2016)
    Abstract Background Timothy (Phleum pratense L.), a cool-season hexaploid perennial, is the most important forage grass species in Nordic countries. Earlier analyses of genetic diversity in a collection of 96 genebank accessions of timothy with SSR markers demonstrated high levels of diversity but could not resolve population structure. Therefore, we examined a subset of 51 accessions with REMAP markers, which are based on retrotransposons, and compared the diversity results with those obtained with SSR markers. Results Using four primer combinations, 533 REMAP markers were analyzed, compared with 464 polymorphic alleles in the 13 SSR loci previously. The average marker index, which describes information obtained per experiment (per primer combination or locus) was over six times higher with REMAPs. Most of the variation found was within accessions, with somewhat less, 89 %, for REMAPs, than for SSR, with 93 %. Conclusions SSRs revealed differences in the level of diversity slightly better than REMAPs but neither marker type could reveal any clear clustering of accessions based on countries, vegetation zones, or different cultivar types. In our study, reliable evaluation of SSR allele dosages was not possible, so each allele had to be handled as a dominant marker. SSR and REMAP, which report from different mechanisms of generating genetic diversity and from different genomic regions, together indicate a lack of population structure. Taken together, this likely reflects the outcrossing and hexaploid nature of timothy rather than failures of either marker system.
  • Trebichalsky, Andrej; Kalendar, Ruslan; Schulman, Alan; Stratula, Olga; Galova, Zdenka; Balazova, Zelmira; Chnapek, Milan (2013)
  • Abdollahi Mandoulakani, Babak; Yaniv, Elitsur; Kalendar, Ruslan; Raats, Dina; Bariana, Harbans S.; Reza Bihamta, Mohammad; Schulman, Alan (Springer, 2015)
    Stripe rust (Pucinia striformis f.sp. tritici) is one of the most important fungal diseases of wheat, found on all continents and in over 60 countries. Wild emmer wheat, Triticum dicoccoides, which is the tetraploid progenitor of durum wheat, is a valuable source of novel stripe rust resistance genes for wheat breeding. T. dicoccoides G25 accession carries Yr15, a gene on chromosome arm 1BS. Yr15 confers resistance to all known stripe rust isolates; it is also effective in introgressed durum and bread wheat. Retrotransposons generate polymorphic insertions, which can be scored as Mendelian markers with techniques including REMAP and IRAP. Six REMAP and IRAP-derived SCAR markers were developed using 1256 F2 plants derived from crosses of the susceptible T. durum accession D447 with its resistant BC3F9 and BC3F10 (B9 and B10) near isogenic lines, which carried Yr15 introgressed from G25. The nearest markers segregated 0.1 cM proximally and 1.1 cM distally to Yr15. These markers were also mapped and validated at the same position in another independent 500 F2 plants derived from crosses of B9 and B10 with the susceptible cultivar Langdon. SCAR270 and SCAR790, surrounding Yr15 at an interval of 1.2 cM, were found to be reliable and robust co-dominant markers in a wide range of wheat lines and cultivars with and without Yr15. These markers are useful tags in marker-assisted wheat breeding programs aiming to incorporate Yr15 into elite wheat lines and cultivars for durable and broad-spectrum resistance against stripe rust.
  • Hosid, Elena; Brodsky, Leonid; Kalendar, Ruslan; Raskina, Olga; Belyayev, Alexander (Genetics Society of America, 2012)
    Background: The environment can have a decisive influence on the structure of the genome, changing it in a certain direction. Therefore, the genomic distribution of environmentally sensitive transposable elements may vary measurably across a species area. In the present research, we aimed to detect and evaluate the level of LTR retrotransposon intraspecific variability in Aegilops speltoides (2n=2x=14), a wild cross-pollinated relative of cultivated wheat. Results: The inter-retrotransposon amplified polymorphism (IRAP) protocol was applied to detect and evaluate the level of LTR retrotransposon intraspecific variability in Ae. speltoides and closely related species of sect. Sitopsis. IRAP analysis revealed significant diversity in TE distribution. Various genotypes from the same population significantly differ with respect to the patterns of the four explored LTR retrotransposons (WIS2, Wilma, Daniela, and Fatima). This diversity points to a constant ongoing process of LTR retrotransposon fraction restructuring in populations of Ae. speltoides throughout the species’ range and within single populations in time. Maximum changes were recorded in genotypes from small stressed populations. Principal component analysis showed that the dynamics of the Fatima element in populations of Ae. speltoides significantly differ from those of WIS2, Wilma, and Daniela. In terms of relationships between Sitopsis species, IRAP analysis of WIS2, Wilma, and Daniela elements revealed a grouping similar to groupings determined by other methods, with Ae. sharonensis and Ae. longissima forming a separate unit, Ae. speltoides appearing as a dispersed group, and Ae. bicornis being in an intermediate position. Conclusions: IRAP display data revealed dynamic changes in LTR retrotransposon fractions in the genome of Ae. speltoides. The process is permanent and population-specific, ultimately leading to the separation of small stressed populations from the main bunch.
  • Bublyk, Olena M.; Andreev, Igor O.; Kalendar, Ruslan; Spiridonova, Kateryna V.; Kunakh, Viktor A. (Springer-Verlag, 2013)
  • Kalendar, Ruslan; Lee, David; Schulman, Alan (Humana Press, 2014)
    Methods in Molecular Biology
    This chapter introduces the software FastPCR as an integrated tools environment for PCR primer and probe design. It also predicts oligonucleotide properties based on experimental studies of PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, group-specific, unique, and overlap extension PCR for multi-fragment assembly in cloning, as well as bisulphite modification assays. It includes a programme to design oligonucleotide sets for long sequence assembly by the ligase chain reaction. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications, provides analyses for a set of primers with prediction of oligonucleotide properties, dimer and G/C-quadruplex detection, linguistic complexity, and provides a dilution and resuspension calculator. The program includes various bioinformatics tools for analysis of sequences with GC or AT skew, of CG content and purine-pyrimidine skew, and of linguistic sequence complexity. It also permits generation of random DNA sequence and analysis of restriction enzymes of all types. It finds or creates restriction enzyme recognition sites for coding sequences and supports the clustering of sequences. It generates consensus sequences and analyses sequence conservation. It performs efficient and complete detection of various repeat types and displays them. FastPCR allows for sequence file batch processing, which is essential for automation. The FastPCR software is available for download at and online version at
  • Stratula, Olga; Cockram, James; Kalendar, Ruslan (Novi Sad Institute of Field and Vegetable Crops, 2014)
    The proteins encoded by cereal β-amylase genes bamy1 and bamy2 genes play an important role in seedling germination and in the brewing process. Here, we use exon-primed intron-crossing (EPIC) to analyse Bmy1 and Bmy2 genetic diversity among 38 accessions belonging to six Poaceae tribes. DNA sequence alignment of multiple Poaceae species β-amylase sequences allowed design of EPIC primers that simultaneously amplify Bmy1 and Bmy2 in all the cereal species investigated. The genetic variation observed in the samples investigated is analysed and discussed, and illustrates the effectiveness of this approach for intra- and interspecific analysis in plant species.
  • Muterko, Alexandr; Kalendar, Ruslan; Salina, Elena (BIOMED CENTRAL LTD, 2016)
    In wheat, the vernalization requirement is mainly controlled by the VRN genes. Different species of hexaploid and tetraploid wheat are widely used as genetic source for new mutant variants and alleles for fundamental investigations and practical breeding programs. In this study, VRN-A1 and VRN-B1 were analysed for 178 accessions representing six tetraploid wheat species (Triticum dicoccoides, T. dicoccum, T. turgidum, T. polonicum, T. carthlicum, T. durum) and five hexaploid species (T. compactum, T. sphaerococcum, T. spelta, T. macha, T. vavilovii).
  • Muterko, Alexandr; Balashova, Irina; Cockram, James; Kalendar, Ruslan; Sivolap, Yuri (SPRINGER NEW YORK LLC, 2015)
    Vernalization requirement in hexaploid bread wheat (Triticum aestivum L.) is largely controlled by a series of homoeologous VERNALIZATION (VRN) genes, VRN-A1, VRN-B1 and VRN-D1. Here we analyse sequence from the promoter and first intron of VRN-D1 in 77 hexaploid accessions, representing five wheat species (T. compactum, T. sphaerococcum, T. spelta, T. vavilovii and T. macha) from different eco-geographic areas within 35 countries. Polymorphism was detected for promoter area of VRN-D1 gene. This polymorphism was caused by mutations which are associated with a new haplotype of the Vrn-D1 gene. Analysis of VRN-D1 intron-1 revealed a novel insertional mutation within the ‘vernalization critical’ region in T. spelta and T. compactum. This allelic variant, termed here Vrn-D1s, is predicted to result in vernalization non-responsive alleles. Analysis of the 844 bp insertion revealed it to be a novel transposable DNA-element not previously described in Triticum (DTA_Chimera_KF800714), belonging to the hAT superfamily. Lastly, we describe a PCR-based assay that discriminates the wild-type vrn-D1 allele from the predicted spring Vrn-D1s allele.
  • Moisy, Cedric; Schulman, Alan H.; Kalendar, Ruslan; Buchmann, Jan P.; Pelsy, Frédérique (Springer, 2014)
    Retrotransposons are ubiquitous throughout the genomes of the vascular plants, but individual retrotransposon families tend to be confined to the level of plant genus or at most family. This restricts the general applicability of a family as molecular markers. Here, we characterize a new plant retrotransposon named Tvv1_Sdem, a member of the Copia superfamily of LTR retrotransposons, from the genome of the wild potato Solanum demissum. Comparative analyses based on structure and sequence showed a high level of similarity of Tvv1_Sdem with Tvv1-VB, a retrotransposon previously described in the grapevine genome Vitis vinifera. Extending the analysis to other species by in silico and in vitro approaches revealed the presence of Tvv1 family members in potato, tomato, and poplar genomes, and led to the identification of full-length copies of Tvv1 in these species. We were also able to identify polymorphism in UTL sequences between Tvv1_Sdem copies from wild and cultivated potatoes that are useful as molecular markers. Combining different approaches, our results suggest that the Tvv1 family of retrotransposons has a monophyletic origin and has been maintained in both the rosids and the asterids, the major clades of dicotyledonous plants, since their divergence about 100 MYA. To our knowledge, Tvv1 represents an unusual plant retrotransposon metapopulation comprising highly similar members disjointedly dispersed among very distant species. The twin features of Tvv1 presence in evolutionarily distant genomes and the diversity of its UTL region in each species make it useful as a source of robust molecular markers for diversity studies and breeding.
  • Kalendar, Ruslan (Novi Sad Institute of Field and Vegetable Crops, 2011)
    Molecular markers play an essential role in all aspects of genetics, modern plant breeding, in human forensics, for map-based cloning of genes, ranging from the identification of genes responsible for desired traits to the management of backcrossing programs. Retrotransposons are well suited as molecular markers. As dispersed and ubiquitous transposable elements, their “copy and paste” life cycle of replicative transposition leads to new genome insertions without excision of the original element. Both the overall structure of retrotransposons and the domains responsible for the various phases of their replication are highly conserved in all eukaryotes. Following the demonstration that retrotransposons are ubiquitous, active, and abundant in plant genomes, various marker systems were developed to exploit polymorphisms in retrotransposon insertion patterns. This review provides an insight into the spectrum of retrotransposon-based marker systems developed for plant species and evaluates the contributions of retrotransposon markers to the analysis of genetic diversity in plants and the way for the rapid isolation of retrotransposon termini.
  • Baranova, Tatyana; Kalendar, Ruslan; Kalaev, V (V. N. Sukachev Institute of Forest, Russian Academy of Sciences, Siberian Branch, 2014)
    The first and second internal transcribed spacer (ITS1 and ITS2) regions of the ribosomal DNA and 5.8S rRNA gene from Rhododendron L. were analysed. This study reveals phylogenetic relationships and collation of data on the phylogeny of the genus Rhododendron L . according to the research of other authors using molecular and classical methods. Sequence analysis of ribosomal spacer showed low variability between species of the genus Rhododendron series of Dauricum. Rh. mucronulatum Turcz., Rh. dauricum L. and some other studied species had identical nucleotide ITS1-ITS2 sequence indicating the artificial division into separate species. Found species differing from each other by 1-2 or few nucleotides, which allows assuming their common phylogenetic affiliation or excluding one taxonomic unit. According to the analysis of ITS1-ITS2 sequences identified 16 groups of species with similar sequence ITS1-ITS2. When comparing the morphological descriptions of some species of the genus Rhododendron L. with a similar sequence of ITS1-ITS2 marked their small differences. Based on the results of molecular genetic analysis it has been assumed that Rhododendron dauricum L., Rh. ledebourii Pojark, Rh. sichotense Pojark and Rh. mucronulatum Turcz belong to the same species. The establishment phylogenetic relationships based on sequence ITS1-ITS2, applicable only in respect of highly isolated species Rhododendron L. To clarify the phylogenetic relationships of the genus Rhododendron L. necessary to expand the comparative analysis of the DNA sequences of universal genes or complex repeats elements (retrotransposons).
  • Belyayev, Alexander; Kalendar, Ruslan; Brodsky, Leonid; Nevo, Eviatar; Schulman, Alan; Raskina, Olga (2010)
    Background<br/>How new forms arise in nature has engaged evolutionary biologists since Darwin's seminal treatise on the origin of species. Transposable elements (TEs) may be among the most important internal sources for intraspecific variability. Thus, we aimed to explore the temporal dynamics of several TEs in individual genotypes from a small, marginal population of Aegilops speltoides. A diploid cross-pollinated grass species, it is a wild relative of the various wheat species known for their large genome sizes contributed by an extraordinary number of TEs, particularly long terminal repeat (LTR) retrotransposons. The population is characterized by high heteromorphy and possesses a wide spectrum of chromosomal abnormalities including supernumerary chromosomes, heterozygosity for translocations, and variability in the chromosomal position or number of 45S and 5S ribosomal DNA (rDNA) sites. We propose that variability on the morphological and chromosomal levels may be linked to variability at the molecular level and particularly in TE proliferation. <br/><br/>Results<br/>Significant temporal fluctuation in the copy number of TEs was detected when processes that take place in small, marginal populations were simulated. It is known that under critical external conditions, outcrossing plants very often transit to self-pollination. Thus, three morphologically different genotypes with chromosomal aberrations were taken from a wild population of Ae. speltoides, and the dynamics of the TE complex traced through three rounds of selfing. It was discovered that: (i) various families of TEs vary tremendously in copy number between individuals from the same population and the selfed progenies; (ii) the fluctuations in copy number are TE-family specific; (iii) there is a great difference in TE copy number expansion or contraction between gametophytes and sporophytes; and (iv) a small percentage of TEs that increase in copy number can actually insert at novel locations and could serve as a bona fide mutagen. <br/><br/>Conclusions<br/>We hypothesize that TE dynamics could promote or intensify morphological and karyotypical changes, some of which may be potentially important for the process of microevolution, and allow species with plastic genomes to survive as new forms or even species in times of rapid climatic change.
  • Kalendar, Ruslan; Schulman, Alan (Humana Press, 2014)
    Methods in Molecular Biology
    Retrotransposons are a major component of virtually all eukaryotic genomes, which makes them useful as molecular markers. 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. To detect polymorphisms for retrotransposon insertions, marker systems generally rely on PCR amplification between the retrotransposon termini and some component of flanking genomic DNA. The main methods of IRAP, REMAP, RBIP, and SSAP all detect the polymorphic sites at which the retrotransposon DNA is integrated into the genome. Marker systems exploiting these methods can be easily developed and are inexpensively deployed in the absence of extensive genome sequence data. Here, we describe protocols for the IRAP, REMAP and iPBS techniques, including methods for PCR amplification with a single primer or with two primers, agarose gel electrophoresis of the product using optimal electrophoresis buffers, we also describe iPBS techniques for the rapid isolation of retrotransposon termini and full-length elements.
  • Boronnikova, Svetlana; Kalendar, Ruslan (M A I K NAUKA - INTERPERIODICA, 2010)
    Species specific LTR retrotransposons were first cloned in five rare relic species of drug plants located in the Perm’ region. Sequences of LTR retrotransposons were used for PCR analysis based on amplification of repeated sequences from LTR or other sites of retrotransposons (IRAP). Genetic diversity was studied in six populations of rare relic species of plants Adonis vernalis L. by means of the IRAP method; 125 polymorphic IRAP markers were analyzed. Parameters for DNA polymorphism and genetic diversity of A. vernalis populations were determined.