Abstract
Transposable elements (TE) represent a major fraction of eukaryotic genomes and play many roles in plant epigenetics. In this chapter, we describe the use of Sequence-Specific Amplified Polymorphism (SSAP) as a reliable Transposon Display technique applicable for use in many plant species. We also discuss the interpretation of SSAP data and associated risks. This technique has potential to allow rapid screening of plant populations, especially in nonmodel or wild species.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Gaut BS, Ross-Ibarra J (2008) Selection on major components of angiosperm genomes. Science 320:484–486
McClintock B (1984) The significance of responses of the genome to challenge. Science 16:792–801
Kato M, Miura A, Bender J, Jacobsen SE, Kakutani T (2003) Role of CG and non-CG methylation in immobilization of transposons in Arabidopsis. Curr Biol 13:421–426
Michalak P (2009) Epigenetic, transposon and small RNA determinants of hybrid dysfunctions. Heredity 102:45–50
Parisod C, Alix K, Just J, Petit M, Sarilar V, Mhiri C, Ainouche M, Chalhoub B, Grandbastien MA (2010) Impact of transposable elements on the organization and function of allopolyploid genomes. New Phytol 186:37–45
Kalendar R, Flavell A, Ellis TH, Sjakste T, Moisy C, Schulman AH (2011) Analysis of plant diversity with retrotransposon-based molecular markers. Heredity 106:520–530
Waugh R, McLean K, Flavell AJ, Pearce SR, Kumar A, Thomas BBT, Powell W (1997) Genetic distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (SSAP). Mol Gen Genet 253:687–694
Syed NH, Flavell AJ (2006) Sequence-specific amplification polymorphisms (SSAPs): a multi-locus approach for analyzing transposon insertions. Nat Protoc 1:2746–2752
Melayah D, Lim KY, Bonnivard E, Chalhoub B, De Borne FD, Mhiri C, Leitch AR, Grandbastien MA (2004) Distribution of the Tnt1 retrotransposon family in the amphidiploid tobacco (Nicotiana tabacum) and its wild Nicotiana relatives. Biol J Linn Soc 82: 639–649
Petit M, Lim KY, Julio E, Poncet C, de Borne FD, Kovarik A, Leitch AR, Grandbastien MA, Mhiri C (2007) Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum). Mol Gen Genet 278:1–15
Sanz AM, Gonzalez SG, Syed NH, Suso MJ, Saldana CC, Flavell AJ (2007) Genetic diversity analysis in Vicia species using retrotransposon-based SSAP markers. Mol Gen Genet 278:433–441
Tam SM, Mhiri C, Vogelaar A, Kerkveld M, Pearce SR, Grandbastien MA (2005) Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor Appl Genet 110:819–831
Petit M, Guidat C, Daniel J, Denis E, Montoriol E, Bui QT, Lim KY, Kovarik A, Leitch AR, Grandbastien MA, Mhiri C (2010) Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol 186:135–147
Tam S, Mhiri C, Grandbastien M-A (2006) Transposable elements and the analysis of plant biodiversity. In: Morot-Gaudry J, Lea P, Briat J (eds) Functional plant genomics. Sciences Publishers, Enfield, NH, pp 529–558
Parisod C, Salmon A, Zerjal T, Tenaillon M, Grandbastien MA, Ainouche ML (2009) Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytol 184:1003–1015
Kashkush K, Khasdan V (2007) Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 177:1975–1985
Cervera MT, Ruiz-Garcia L, Martinez-Zapater JM (2002) Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. Mol Genet Genomics 268:543–552
Shaked H, Kashkush K, Ozkan H, Feldman M, Levy AA (2001) Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat. Plant Cell 13:1749–1759
Takata M, Kiyohara A, Takasu A, Kishima Y, Ohtsubo H, Sano Y (2007) Rice transposable elements are characterized by various methylation environments in the genome. BMC Genomics 8:469
Roberts RJ, Vincze T, Posfai J, Macelis D (2010) REBASE—a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 38:D234–D236
Salmon A, Ainouche ML, Wendel JF (2005) Genetic and epigenetic consequences of recent hybridization and polyploidy in Spartina (Poaceae). Mol Ecol 14:1163–1175
Bonin A, Bellemain E, Eidesen PB, Pompanon F, Brochmann C, Taberlet P (2004) How to track and assess genotyping errors in population genetics studies. Mol Ecol 13:3261–3273
Pompanon F, Bonin A, Bellemain E, Taberlet P (2005) Genotyping errors: causes, consequences and solutions. Nat Rev Genet 6: 847–859
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media, New York
About this protocol
Cite this protocol
Parisod, C., Salmon, A., Ainouche, M., Grandbastien, MA. (2014). Detecting Epigenetic Effects of Transposable Elements in Plants. In: Spillane, C., McKeown, P. (eds) Plant Epigenetics and Epigenomics. Methods in Molecular Biology, vol 1112. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-773-0_14
Download citation
DOI: https://doi.org/10.1007/978-1-62703-773-0_14
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-772-3
Online ISBN: 978-1-62703-773-0
eBook Packages: Springer Protocols