Ruslan Kalendar

Summary

Affiliation: University of Helsinki
Location: Helsinki, Finland
URL: http://www.helsinki.fi/people/Ruslan.Kalendar/
Summary:
general evolution, Goethes science, genetics, retrotransposons, RNA world, plant molecular genetics research and DNA markers, bioinformatics

Publications

  1. pmc Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat
    Alexander Belyayev
    Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel
    Mob DNA 1:6. 2010
  2. ncbi request reprint [The genetic polymorphism of cereals demonstrated by PCR with random primers]
    Iu M Sivolap
    Tsitol Genet 28:54-61. 1994
  3. ncbi request reprint IRAP and REMAP for retrotransposon-based genotyping and fingerprinting
    Ruslan Kalendar
    MTT BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P O Box 56, Viikinkaari 4, FIN 00014 Helsinki, Finland
    Nat Protoc 1:2478-84. 2006
  4. ncbi request reprint Mapping of major spot-type and net-type net-blotch resistance genes in the Ethiopian barley line CI 9819
    O M Manninen
    MTT Agrifood Research Finland, Biotechnology and Food Research, Myllytie 10, FIN 31600 Jokioinen, Finland
    Genome 49:1564-71. 2006
  5. ncbi request reprint A major gene for grain cadmium accumulation in oat (Avena sativa L.)
    Pirjo Tanhuanpää
    Plant Genomics, Biotechnology and Food Research, MTT Agrifood Research Finland, FI 31600 Jokioinen, Finland
    Genome 50:588-94. 2007
  6. ncbi request reprint Reme1, a Copia retrotransposon in melon, is transcriptionally induced by UV light
    Elisenda Ramallo
    Department of Molecular Genetics, Consorci CSIC IRTA, Jordi Girona 18 26, 08034 Barcelona, Spain
    Plant Mol Biol 66:137-50. 2008
  7. pmc Cassandra retrotransposons carry independently transcribed 5S RNA
    Ruslan Kalendar
    MTT BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, FIN 00014, Helsinki, Finland
    Proc Natl Acad Sci U S A 105:5833-8. 2008
  8. doi request reprint The first doubled haploid linkage map for cultivated oat
    Pirjo Tanhuanpää
    Plant Genomics, Biotechnology and Food Research, MTT Agrifood Research Finland, FI 31600 Jokioinen, Finland
    Genome 51:560-9. 2008
  9. doi request reprint Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent
    P Smykal
    AGRITEC Plant Research Ltd, Plant Biotechnology Department, Sumperk, Czech Republic
    Heredity (Edinb) 103:157-67. 2009
  10. doi request reprint Genetic variability in sunflower (Helianthus annuus L.) and in the Helianthus genus as assessed by retrotransposon-based molecular markers
    M Vukich
    Department of Crop Plant Biology, Genetics Section, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
    Theor Appl Genet 119:1027-38. 2009

Collaborators

Detail Information

Publications35

  1. pmc Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat
    Alexander Belyayev
    Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel
    Mob DNA 1:6. 2010
    ..We propose that variability on the morphological and chromosomal levels may be linked to variability at the molecular level and particularly in TE proliferation...
  2. ncbi request reprint [The genetic polymorphism of cereals demonstrated by PCR with random primers]
    Iu M Sivolap
    Tsitol Genet 28:54-61. 1994
    ..Optimal temperature conditions and Mg2+ concentrations were determined for studying inter- and intraspecific DNA polymorphism in the most important cereals...
  3. ncbi request reprint IRAP and REMAP for retrotransposon-based genotyping and fingerprinting
    Ruslan Kalendar
    MTT BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P O Box 56, Viikinkaari 4, FIN 00014 Helsinki, Finland
    Nat Protoc 1:2478-84. 2006
    ..This protocol can be completed in 1-2 d...
  4. ncbi request reprint Mapping of major spot-type and net-type net-blotch resistance genes in the Ethiopian barley line CI 9819
    O M Manninen
    MTT Agrifood Research Finland, Biotechnology and Food Research, Myllytie 10, FIN 31600 Jokioinen, Finland
    Genome 49:1564-71. 2006
    ..The Ethiopian 2-rowed barley line CI 9819 thus carries at least 2 independent major genes for net-blotch resistance: Rpt5, active against net-type isolates; and Rpt6, active against specific spot-type isolates...
  5. ncbi request reprint A major gene for grain cadmium accumulation in oat (Avena sativa L.)
    Pirjo Tanhuanpää
    Plant Genomics, Biotechnology and Food Research, MTT Agrifood Research Finland, FI 31600 Jokioinen, Finland
    Genome 50:588-94. 2007
    ..The 4 markers were assigned to 1 linkage group that exhibited a QTL (quantitative trait locus) representing a major gene for grain Cd concentration...
  6. ncbi request reprint Reme1, a Copia retrotransposon in melon, is transcriptionally induced by UV light
    Elisenda Ramallo
    Department of Molecular Genetics, Consorci CSIC IRTA, Jordi Girona 18 26, 08034 Barcelona, Spain
    Plant Mol Biol 66:137-50. 2008
    ..The cDNAs of Reme1 transcripts showed less diversity than do Reme1 genomic sequences, suggesting that a subfamily of these elements is differentially responsive to UV...
  7. pmc Cassandra retrotransposons carry independently transcribed 5S RNA
    Ruslan Kalendar
    MTT BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, FIN 00014, Helsinki, Finland
    Proc Natl Acad Sci U S A 105:5833-8. 2008
    ..Cassandra thus appears both to have adapted a ubiquitous cellular gene for ribosomal RNA for use as a promoter and to parasitize an as-yet-unidentified group of retrotransposons for the proteins needed in its lifecycle...
  8. doi request reprint The first doubled haploid linkage map for cultivated oat
    Pirjo Tanhuanpää
    Plant Genomics, Biotechnology and Food Research, MTT Agrifood Research Finland, FI 31600 Jokioinen, Finland
    Genome 51:560-9. 2008
    ..This is explained by the better performance of 'Aslak' in anther culture. Quantitative trait loci affecting some important quality and agronomic traits are being localized on the map...
  9. doi request reprint Evolutionary conserved lineage of Angela-family retrotransposons as a genome-wide microsatellite repeat dispersal agent
    P Smykal
    AGRITEC Plant Research Ltd, Plant Biotechnology Department, Sumperk, Czech Republic
    Heredity (Edinb) 103:157-67. 2009
    ..The implications of this finding regarding the evolution of SSRs within the genome, as well as their utilization as molecular markers, are discussed...
  10. doi request reprint Genetic variability in sunflower (Helianthus annuus L.) and in the Helianthus genus as assessed by retrotransposon-based molecular markers
    M Vukich
    Department of Crop Plant Biology, Genetics Section, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
    Theor Appl Genet 119:1027-38. 2009
    ..Principal component analysis of IRAP fingerprints allows the distinction between perennial and annual Helianthus species especially when the SURE element is concerned...
  11. ncbi request reprint [Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants]
    S V Boronnikova
    Genetika 46:44-50. 2010
    ..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...
  12. doi request reprint iPBS: a universal method for DNA fingerprinting and retrotransposon isolation
    Ruslan Kalendar
    MTT BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P O Box 65, Helsinki, Finland
    Theor Appl Genet 121:1419-30. 2010
    ..Furthermore, the inter-PBS amplification technique as such has proved to be a powerful DNA fingerprinting technology without the need for prior sequence knowledge...
  13. pmc Analysis of plant diversity with retrotransposon-based molecular markers
    R Kalendar
    MTT BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
    Heredity (Edinb) 106:520-30. 2011
    ..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 population diversity in plants...
  14. doi request reprint A doubled haploid rye linkage map with a QTL affecting α-amylase activity
    Teija Tenhola-Roininen
    Plant Genomics, Biotechnology and Food Research, MTT Agrifood Research Finland, Myllytie 1, Jokioinen, Finland
    J Appl Genet 52:299-304. 2011
    ..The QTL was localized on the long arm of chromosome 5R. Microsatellites SCM74, RMS1115, and SCM77, nearest to the QTL, can be used for marker-assisted selection as a part of a rye breeding program to decrease sprouting damage...
  15. doi request reprint Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers
    P Smykal
    Plant Biotechnology Department, AGRITEC Plant Research Ltd, Sumperk, Czech Republic
    Theor Appl Genet 122:1385-97. 2011
    ..These findings provide a basis for better flax germplasm management, core collection establishment, and exploration of diversity in breeding, as well as for exploration of the role of retrotransposons in flax genome dynamics...
  16. doi request reprint Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analysis
    Ruslan Kalendar
    MTT BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, P O Box 65, FIN 00014 Helsinki, Finland
    Genomics 98:137-44. 2011
    ....
  17. ncbi request reprint [IRAP-and REMAP-analyses of barley varieties of Odessa breeding]
    A F Brik
    Tsitol Genet 40:24-33. 2006
    ..The detailed genotype formulas are represented which reflect the intravariety polimorphism and make it possible to detect the changes in variety structure in the course of seed production process...
  18. ncbi request reprint Generation of SNP markers for short straw in oat (Avena sativa L.)
    Pirjo Tanhuanpää
    Crops and Biotechnology, Plant Production Research, MTT Agrifood Research Finland, FIN 31600 Jokioinen, Finland
    Genome 49:282-7. 2006
    ..2 and 12.6 cM from Dw6, respectively. They can be used in future efforts both to enhance oat germplasm by application of molecular markers and to determine the nature of the gene through positional cloning...
  19. ncbi request reprint TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports
    Kristiina Antonius-Klemola
    MTT Agrifood Research Finland Crops and Biotechnology, 31600 Jokioinen, Finland
    Theor Appl Genet 112:999-1008. 2006
    ....
  20. ncbi request reprint [Genetic polymorphism in barley detected by arbitrary primers]
    Iu M Sivolap
    Genetika 31:1358-64. 1995
    ..The dendrogram of relations between species from the genus Hordeum and species of some cultivated cereals was constructed on the basis of RAPD analysis...
  21. ncbi request reprint Phylogeny and transpositional activity of Ty1-copia group retrotransposons in cereal genomes
    B M Gribbon
    Department of Biochemistry, University of Dundee, Scotland, UK
    Mol Gen Genet 261:883-91. 1999
    ..Both transposons are highly polymorphic within all species tested. These data suggest that transposition proficiency may be a common and evolutionarily stable feature of the Ty1-copia group retrotransposons of cereal grasses...
  22. pmc Genome evolution of wild barley (Hordeum spontaneum) by BARE-1 retrotransposon dynamics in response to sharp microclimatic divergence
    R Kalendar
    Institute of Biotechnology, University of Helsinki, Plant Genomics Laboratory, Viikki Biocenter, P O Box 56, FIN 00014 Helsinki, Finland
    Proc Natl Acad Sci U S A 97:6603-7. 2000
    ..These local data are consistent with regional trends for BARE-1 in H. spontaneum across Israel and therefore may reflect adaptive selection for increasing genome size through retrotransposon activity...
  23. ncbi request reprint Structure, functionality, and evolution of the BARE-1 retrotransposon of barley
    C M Vicient
    Institute of Biotechnology, University of Helsinki, Plant Genomics Laboratory, Viikki Biocenter, Finland
    Genetica 107:53-63. 1999
    ..New techniques have been developed which exploit the insertion site polymorphism generated by BARE-1 integration to produce molecular markers for breeding, biodiversity, and mapping applications...
  24. ncbi request reprint [The mapping of the barley genome by RAPD analysis using double haploid strains]
    Iu Iu Sulima
    Tsitol Genet 34:41-9. 2000
    ..The distribution of the markers was analyzed, comparison with other published maps was made. Some statistical considerations are presented. Alternative strategies of gene mapping are considered...
  25. ncbi request reprint Application of BARE-1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley
    O Manninen
    Institute of Biotechnology, University of Helsinki, Plant Genomics Laboratory, Viikki Biocenter, Finland
    Mol Gen Genet 264:325-34. 2000
    ..The type and local density of the markers should facilitate future map-based cloning of the resistance gene as well as manipulation of the resistance through backcross breeding...
  26. pmc Active retrotransposons are a common feature of grass genomes
    C M Vicient
    Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 56, Viikinkaari 6, FIN-00014 Helsinki, Finland
    Plant Physiol 125:1283-92. 2001
    ....
  27. pmc Envelope-class retrovirus-like elements are widespread, transcribed and spliced, and insertionally polymorphic in plants
    C M Vicient
    Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Viikki Biocenter, FIN-00014 Helsinki, Finland
    Genome Res 11:2041-9. 2001
    ..The putative ENV polypeptides of Bagy-2 and rice Rigy-2 contain predicted leucine zipper and transmembrane domains typical of retroviral ENVs. These findings raise the prospect of active retroviral agents among the plants...
  28. ncbi request reprint A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function
    Elena Boyko
    Wheat Genetics Resource Center, Kansas State University, Manhattan 66506 5502, USA
    Plant Mol Biol 48:767-90. 2002
    ..Most of the positive interference was restricted to the long arms. The model of chromosome structure and function in cereals with large genomes that emerges from these studies is discussed...
  29. ncbi request reprint Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica C.E. Hubbard (Poaceae)
    Alex Baumel
    Population, Species and Evolution Lab, UMR CNRS 6553, University of Rennes 1 Campus Scientifique de Beaulieu, Rennes Cedex, France
    Mol Biol Evol 19:1218-27. 2002
    ..anglica has not undergone extensive changes since its formation. This contrasts with previous results from the literature, which report rapid structural changes in experimentally resynthesized allopolyploids...
  30. ncbi request reprint Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques
    F Leigh
    Molecular Research Group, NIAB, Huntingdon Road, Cambridge CB3 0LE, UK
    Mol Genet Genomics 269:464-74. 2003
    ....
  31. pmc Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes
    Ruslan Kalendar
    MTT BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, FIN 00014 Helsinki, Finland
    Genetics 166:1437-50. 2004
    ..They are dispersed throughout the genome in an estimated 1.3 x 10(3) full-length copies and 1.16 x 10(4) solo LTRs, indicating frequent recombinational loss of internal domains as demonstrated also for the BARE-1 barley retrotransposon...
  32. ncbi request reprint Variability, recombination, and mosaic evolution of the barley BARE-1 retrotransposon
    Carlos M Vicient
    MTT BI Plant Genomics Laboratory, Institute of Biotechnology, University of Helsinki, Helsinki, FIN 00014, Finland
    J Mol Evol 61:275-91. 2005
    ..The data indicate that recombination contributes to the complexity and plasticity of retroelement evolution in plant genomes...
  33. ncbi request reprint A movable feast: diverse retrotransposons and their contribution to barley genome dynamics
    A H Schulman
    Plant Breeding Biotechnology, MTT Agrifood Research, Jokioinen, Finland
    Cytogenet Genome Res 110:598-605. 2005
    ..The sequence conservation and integrative capacity of barley retrotransposons have made them excellent sources for development of molecular marker systems...
  34. pmc Diversity of long terminal repeat retrotransposon genome distribution in natural populations of the wild diploid wheat Aegilops speltoides
    Elena Hosid
    Institute of Evolution, University of Haifa, Mount Carmel, 31905 Haifa, Israel
    Genetics 190:263-74. 2012
    ..speltoides. The process is permanent and population specific, ultimately leading to the separation of small stressed populations from the main group...