Open Access

Development and Characterisation of Irap Markers From Expressed Retrotransposon-like sequences in Pinus sylvestris L.


Cite

Asif, J. M., Othman, F. Y. (2005). Characterization of fusarium wilt-resistant and fusarium wilt-susceptible somaclones of banana cultivar Rastali (Musa AAB) by random amplified polymorphic DNA and retrotransposon markers. Plant Mol. Biol. Rep., 23 (3), 241–249.Search in Google Scholar

Bairu, M. W., Aremu, A. O., Staden, J. V. (2011). Somaclonal variation in plants: Causes and detection methods. Plant Growth Regul., 63, 147–173.10.1007/s10725-010-9554-xSearch in Google Scholar

Baranek, M., Meszaros, M., Sochorova, J., Cechova, J., Raddova, J. (2012). Utility of retrotransposon-derived marker systems for differentiation of presumed clones of the apricot cultivar Velkopavlovická. Sci. Horticult., 143, 1–6.10.1016/j.scienta.2012.05.022Search in Google Scholar

Bayram, E., Yilmaz, S., Hamat-Mecbur, H., Kartal-Alacam, G., Gozukirmizi, N. (2012). Nikita retrotransposon movements in callus cultures of barley (Hordeum vulgare L.). Plant Omics Journal (POJ), 5 (3), 211–215.Search in Google Scholar

Benachenhou, F., Sperber, G. O., Bongcam-Rudloff, E., Andersson, G., Boeke, J. D., Blomberg, J. (2013). Conserved structure and inferred evolutionary history of long terminal repeats (LTRs). Mobile DNA, doi: 10.1186/1759-8753-4-5.10.1186/1759-8753-4-5360100323369192Search in Google Scholar

Berg, D. E., Howe, M. H. (eds.) (1989). Mobile DNA. Washington, D.C.: American Society for Microbiology Press.Search in Google Scholar

Birnboim, H. C., Doly, J. (1979). A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucl. Acids Res., 7 (6), 1513–1523.10.1093/nar/7.6.1513342324388356Search in Google Scholar

Brandes, A., Heslop-Harrison, J. S., Kamm, A., Kubis, S., Doudrick, R. L., Schmidt, T. (1997). Comparative analysis of the chromosomal and genomic organization of Ty1-copia -like retrotransposons in pteridophytes, gymnosperms and angiosperms. Plant Mol. Biol., 33 (1), 11–21.10.1023/A:1005797222148Search in Google Scholar

Campbell, B. C., LeMare, S., Piperidis, G., Godwin, I. D. (2011). IRAP, a retrotransposon-based marker system for the detection of somaclonal variation in barley. Mol. Breed., 27, 193–206.10.1007/s11032-010-9422-4Search in Google Scholar

Capy, P. (2005). Classification and nomenclature of retrotransposable elements. Cytogenet. Gen. Res., 110 (1–4), 457–461.10.1159/00008497816093698Search in Google Scholar

Capy, P., Gasperi, G., Biemont, C., Bazin, C. (2000). Stress and transposable elements: Co-evolution or useful parasites? Heredity, 85, 101–106.10.1046/j.1365-2540.2000.00751.x11012710Search in Google Scholar

Carvalho, A., Guedes-Pinto, H., Lima-Brito, J. E. (2012). Genetic diversity in old Portuguese durum wheat cultivars assessed by retrotransposon-based markers. Plant Mol. Biol. Rep., 30, 578–589.10.1007/s11105-011-0367-5Search in Google Scholar

Castro, I., D’Onofrio, C., Martín, J. P., Ortiz, J. M., De Lorenzis, G., Ferreira, V., Pinto-Carnide, O. (2012). Effectiveness of AFLPs and retrotransposon-based markers for the identification of Portuguese grapevine cultivars and clones. Mol. Biotechnol., 52 (1), 26–39.10.1007/s12033-011-9470-y22081367Search in Google Scholar

D’Onofrio, C., De Lorenzis, G., Giordani, T., Natali, L., Cavallini, A., Scalabrelli, G. (2010). Retrotransposon-based molecular markers for grapevine species and cultivars identification. Tree Genet. Gen., 6, 451–466.10.1007/s11295-009-0263-4Search in Google Scholar

Feschotte, C., Jiang, N., Wessler, S. R. (2002). Plant transposable elements: Where genetics meets genomics. Nat. Rev. Genet., 3, 329–341.10.1038/nrg793Search in Google Scholar

Finnegan, D. J. (1989). Eukaryotic transposable elements and genome evolution. Trends. Genet., 5, 103–107.10.1016/0168-9525(89)90039-5Search in Google Scholar

Flavell, A. J., Pearce, S. R., Kumar, A. (1994). Plant transposable elements and the genome. Curr. Opin. Genet. Dev., 4, 838–844.10.1016/0959-437X(94)90068-XSearch in Google Scholar

Friesen, N., Brandes, A., Heslop-Harrison, J. S. (2001). Diversity, origin and distribution of retrotransposons (gypsy and copia) in conifers. Mol. Biol. Evol., 18 (7), 1176–1188.10.1093/oxfordjournals.molbev.a003905Search in Google Scholar

Gao, D., Chen, J., Chen, M., Meyers, B. C., Jackson, S. (2012). A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PloS One, doi:10.1371/journal.pone.0032010.10.1371/journal.pone.0032010Search in Google Scholar

Grandbastien, M. A., Lucas, H., Morel, J. B., Corinne, M. C., Vernhettes, S., Casacuberta, J. M. (1997). The expression of the tobacco Tnt1 retrotransposon is linked to plant defense responses. Genetica, 100, 241–252.10.1023/A:1018302216927Search in Google Scholar

Inoue, H., Nojima, H., Okayama, H. (1990). High efficiency transformation of Escherichia coli with plasmids. Gene, 96, 23–28.10.1016/0378-1119(90)90336-PSearch in Google Scholar

Ito, H., Gaubert, H., Bucher, E., Mirouze, M., Vaillant, I., Paszkowski, J. (2011). An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature, 472, 115–118.10.1038/nature0986121399627Search in Google Scholar

Kalendar, R., Antonius, K., Smykal, P., Schulman, A.H. (2010). iPBS: A universal method for DNA fingerprinting and retrotransposon isolation. Theor. Appl. Genet., doi:10.1007/s00122-010-1398-2.10.1007/s00122-010-1398-220623102Search in Google Scholar

Kalendar, R., Grob, T., Regina, M., Suoniemi, A., Schulman, A. (1999). IRAP and REMAP: Two new retrotransposon-based DNA fingerprinting techniques. Theor. Appl. Genet., 98, 704–711.10.1007/s001220051124Search in Google Scholar

Kalendar, R., Schulman, A. H. (2007). IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nat. Protoc., 1 (5), 2478–2484.Search in Google Scholar

Kamm, A., Doudric, R. L., Heslop-Harrison, J. S., Schmidt, T. (1996). The genomic and physical organization of Ty1-copia -like sequences as a component of large genomes in Pinus elliottii var. elliottii and other gymnosperms. Proc. Natl. Acad. Sci. USA, 93, 2708–2713.10.1073/pnas.93.7.2708Search in Google Scholar

Knight, C. A., Ackerly, D. D. (2002). Variation in nuclear DNA content across environmental gradients: A quantile regression analysis. Ecol. Lett., 5, 66–76.10.1046/j.1461-0248.2002.00283.xSearch in Google Scholar

Kohany, O., Gentles, A. J., Hankus, L., Jurka, J. (2006). Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics, doi:10.1186/1471-2105-7-474.10.1186/1471-2105-7-474Search in Google Scholar

Kossack, D. S., Kinlaw, C. S. (1999). IFG, a gypsy -like retrotransposon in Pinus (Pinaceae), has an extensive history in pines. Plant Mol. Biol., 39, 417–426.10.1023/A:1006115732620Search in Google Scholar

Kovach, A., Wegrzyn, J. L., Parra, G., Holt, C., Bruening, G. E., Loopstra, C. A., Hartigan, J., Yandell, M., Langley, C. H., Korf, I., Neale, D. B. (2010). The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences. BMC Genomics, doi: 10.1186/1471-2164-11-420.10.1186/1471-2164-11-420Search in Google Scholar

Kumar, A., Bennetzen, J. L. (1999). Plant Retrotransposons. Annu. Rev. Genet., 33, 479–532.10.1146/annurev.genet.33.1.479Search in Google Scholar

Kumar, A., Hirochika, H. (2001). Applications of retrotransposons as genetic tools in plant biology. Trends Plant Sci., 6 (3), 127–134.10.1016/S1360-1385(00)01860-4Search in Google Scholar

Kumar, A., Pearce, S. R., McLean, K., Harrison, G., Heslop-Harrison, J. S., Waugh, R., Flavell, A. J. (1997). The Ty1-copia group of retrotransposons in plants: Genomic organisation, evolution, and use as molecular markers. Genetica, 100 (1–3), 205–217.10.1007/978-94-011-4898-6_21Search in Google Scholar

L’Homme, Y., Seguin, A., Tremblay, F. M. (2000). Different classes of retrotransposons in coniferous spruce species. Genome, 43, 1084–1089.10.1139/g00-077Search in Google Scholar

Leitch, I. J., Bennett, M. D. (2004). Genome downsizing in polyploid plants. Biol. J. Linn. Soc., 82, 651–663.10.1111/j.1095-8312.2004.00349.xSearch in Google Scholar

Lightbourn, G. J., Jelesko, J. G., Veilleux, R. E. (2007). Retrotransposonbased markers from potato monoploids used in somatic hybridization. Genome, 50 (5), 492–501.10.1139/G07-026Search in Google Scholar

Mak, J., Kleiman, L. (1997). Primer tRNAs for reverse transcription. J. Virol., 71 (11), 8087–8095.10.1128/jvi.71.11.8087-8095.1997Search in Google Scholar

McClintock, B. (1984). The significance of responses of the genome to challenge. Science, 226, 792–801.10.1126/science.1573926015739260Search in Google Scholar

Mignone, F., Grillo, G., Licciulli, F., Iacono, M., Liuni, S., Kersey, P. J., Duarte, J., Saccone, C. Pesole, G. (2005). UTRdb and UTRsite: A collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucl. Acids Res., 33, D141–146.Search in Google Scholar

Miguel, C., Simoes, M., Oliveira, M. M., Rocheta, M. (2008). Envelope-like retrotransposons in the plant kingdom: Evidence of their presence in Gymnosperms (Pinus pinaster). J. Mol. Evol., 67, 517–525.10.1007/s00239-008-9168-318925379Search in Google Scholar

Murray, B.G. (1998). Nuclear DNA amounts in gymnosperms. Ann. Bot., 82, 3–15.10.1006/anbo.1998.0764Search in Google Scholar

Murray, B.G. (2005). When does intraspecific C-value variation become taxonomically significant? Ann. Bot., 95, 119–125.Search in Google Scholar

Neumann, P., Pozárková, D., Macas, J. (2003). Highly abundant pea LTR Retrotransposon Ogre is constitutively transcribed and partially spliced. Plant. Mol. Biol., 53 (3), 399–410.10.1023/B:PLAN.0000006945.77043.ceSearch in Google Scholar

Nystedt, B., Street, N. R., Wetterbom, A., Zuccolo, A., Lin, Y. C., Scofield, D. G., Vezzi, F., Delhomme, N., Giacomello, S., Alexeyenko, A., Vicedomini, R., Sahlin, K., Sherwood, E., Elfstrand, M., Gramzow, L., Holmberg, K., Hällman, J., Keech, O., Klasson, L., Koriabine, M., Kucukoglu, M., Käller, M., Luthman, J., Lysholm, F., Niittylä, T., Olson, A., Rilakovic, N., Ritland, C., Rosselló, J.A., Sena, J., Svensson, T., Talavera-López, C., Theißen, G., Tuominen, H., Vanneste, K., Wu, Z. Q., Zhang, B., Zerbe, P., Arvestad, L., Bhalerao, R., Bohlmann, J., Bousquet, J., Garcia, G. R., Hvidsten, T. R., de Jong, P., MacKay, J., Morgante, M., Ritland, K., Sundberg, B., Thompson, S. L., Van de Peer, Y., Andersson, B., Nilsson, O., Ingvarsson, P.K., Lundeberg, J., Jansson, S. (2013). The Norway spruce genome sequence and conifer genome evolution. Nature, doi:10.1038/nature12211.10.1038/nature1221123698360Search in Google Scholar

Peakall, R., Smouse, P. E. (2006). GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Mol. Ecol. Notes, 6, 288–295.10.1111/j.1471-8286.2005.01155.xSearch in Google Scholar

Porebski, S., Bailey, G. L., Baum, B. R. (1997). Modification of a CTAB DNA extraction protocol for plants containing high polysaharide and polyphenol componenets. Plant Mol. Biol. Rep., 15 (1), 8–15.10.1007/BF02772108Search in Google Scholar

Rocheta, M., Cordeiro, J., Oliveira, M., Miguel, C. (2007). PpRT1: The first complete gypsy -like retrotransposon isolated in Pinus pinaster. Planta, 225, 551–562.10.1007/s00425-006-0370-517008993Search in Google Scholar

Saeidi, H., Rahiminejad, M. R., Heslop-Harrison, J. S. (2008). Retroelement insertional polymorphisms, diversity and phylogeography within diploid, D-genome Aegilops tauschii (Triticeae, Poaceae) sub-taxa in Iran. Ann. Bot., 101 (6), 855–861.10.1093/aob/mcn042271020418411258Search in Google Scholar

Schlüter, P. M., Harris, S. A. (2006). Analysis of multilocus fingerprinting data sets containing missing data. Mol. Ecol. Notes, 6, 569–572.10.1111/j.1471-8286.2006.01225.xSearch in Google Scholar

Schulman, A. H. (2007). Molecular markers to assess genetic diversity. Euphytica, 158, 313–321.10.1007/s10681-006-9282-5Search in Google Scholar

Schulman, A. H., Flavell, A. J., Ellis, T. H. (2004). The application of LTR retrotransposons as molecular markers in plants. Meth. Mol. Biol., 260, 145–173.10.1385/1-59259-755-6:145Search in Google Scholar

Schulman, A. H., Flavell, A. J., Paux, E., Ellis, T. H. (2012). The application of LTR retrotransposons as molecular markers in plants. Meth. Mol. Biol., 859, 115–153.10.1007/978-1-61779-603-6_722367869Search in Google Scholar

Solovyev, V. V. (2002). Structure, properties and computer identification of eukaryotic genes. In: Bioinformatics Genomes to Drugs, Basic Technologies (59–111 pp.). Lengauer, T. (ed.). Wiley.Search in Google Scholar

Solovyev, V. V., Shahmuradov, I. A. (2003). PromH: Promoters identification using orthologous genomic sequences. Nucl. Acids Res., 31 (13), 3540–3545.10.1093/nar/gkg52516893212824362Search in Google Scholar

Soranzo, N., Provan, J., Powell, W. (1998). Characterization of microsatellite loci in Pinus sylvestris L. Mol. Ecol., 7, 1247–1263.Search in Google Scholar

Stuart-Rogers, C., Flavell, A. J. (2001). The evolution of Ty1-copia group retrotransposons in gymnosperms. Mol. Biol. Evol., 18 (2), 155–163.10.1093/oxfordjournals.molbev.a00378911158374Search in Google Scholar

Subudhi, P., Magpantay, G., Karan, R. (2013) A retrotransposon-based probe for fingerprinting and evolutionary studies in rice (Oryza sativa). Genet. Res. Crop. Evol., 60 (4), 1263–1273.10.1007/s10722-012-9917-4Search in Google Scholar

Tam, S. M., Mhiri, C., Vogelaar, A., Kerkveld, M., Pearce, S. R., Grandbastien, M. A. (2005). Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor. Appl. Genet., 110 (5), 819–831.10.1007/s00122-004-1837-z15700147Search in Google Scholar

Vicient, C. M., Kalendar, R., Schulman, A. H. (2005). Variability, recombination and mosaic evolution of the barley BARE-1 retrotransposon. J. Mol. Evol., 61, 275–291.10.1007/s00239-004-0168-7Search in Google Scholar

Voronova, A., Jansons, A., Ruòìis, D. (2011). Expression of retrotransposon-like sequences in Scots pine (Pinus sylvestris L.) in response to heat stress. Environ. Exper. Biol., 9, 121–127.Search in Google Scholar

Wessler, S. R. (1996). Plant retrotransposons: Turned on by stress. Curr. Biol., 6 (8), 959–961.10.1016/S0960-9822(02)00638-3Search in Google Scholar

Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O., Paux, E., SanMiguel, P., Schulman, A. H. (2007) A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet., 8 (12), 973–982.10.1038/nrg216517984973Search in Google Scholar

Xiong, Y., Eickbush, T. H. (1990). Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J., 9, 3353–3362.10.1002/j.1460-2075.1990.tb07536.xSearch in Google Scholar

Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., Madden, T. (2012). Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics, doi:10.1186/1471-2105-13-134.10.1186/1471-2105-13-134341270222708584Search in Google Scholar

eISSN:
1407-009X
Language:
English
Publication timeframe:
6 times per year
Journal Subjects:
General Interest, Mathematics, General Mathematics