Plant Molecular Biology

, Volume 70, Issue 1–2, pp 17–29 | Cite as

Variation in cytosine methylation patterns during ploidy level conversions in Eragrostis curvula

  • Ana C. Ochogavía
  • Gerardo Cervigni
  • Juan P. Selva
  • Viviana C. Echenique
  • Silvina C. Pessino
Article

Abstract

In many species polyploidization involves rearrangements of the progenitor genomes, at both genetic and epigenetic levels. We analyzed the cytosine methylation status in a ‘tetraploid-diploid-tetraploid’ series of Eragrostis curvula with a common genetic background by using the MSAP (Methylation-sensitive Amplified Polymorphism) technique. Considerable levels of polymorphisms were detected during ploidy conversions. The total level of methylation observed was lower in the diploid genotype compared to the tetraploid ones. A significant proportion of the epigenetic modifications occurring during the tetraploid–diploid conversion reverted during the diploid–tetraploid one. Genetic and expression data from previous work were used to analyze correlation with methylation variation. All genetic, epigenetic and gene expression variation data correlated significantly when compared by pairs in simple Mantel tests. Dendrograms reflecting genetic, epigenetic and expression distances as well as principal coordinate analysis suggested that plants of identical ploidy levels present similar sets of data. Twelve (12) different genomic fragments displaying different methylation behavior during the ploidy conversions were isolated, sequenced and characterized.

Keywords

Cytosine methylation Epigenetics Eragrostis curvula Gene expression Genome structure Polyploidy 

Notes

Acknowledgements

Thanks are due to Dr. Paul Voigt for critically reading the manuscript. This work was funded by ANPCyT (Agencia Nacional de Promoción Científica y Tecnológica, Argentina, BID 1201-OC-AR PICT03 14624 and PAV 137). Ana Ochogavía and Juan Pablo Selva are fellows from CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina). Viviana C. Echenique, Gerardo Cervigni and Silvina C. Pessino are career members of CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina).

Supplementary material

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Supplementary material 1 (TIFF 3876 kb)

References

  1. Cardone S, Polci P, Selva JP, Mecchia M, Pessino SC, Herrmann P, Cambi V, Voigt P, Spangenberg G, Echenique V (2006) Novel genotypes of the subtropical grass Eragrostis curvula for the analysis of apomixis (diplospory). Euphytica 151(2):263–272. doi:10.1007/s10681-006-9156-x CrossRefGoogle Scholar
  2. Cervera MT, Ruiz García JM, Martinez Zapater JM (2002) Análisis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. Mol Genet Genomics 268:543–552. doi:10.1007/s00438-002-0772-4 PubMedCrossRefGoogle Scholar
  3. Cervigni GD, Paniego N, Pessino S, Selva JP, Zappacosta D, Spangenberg G, Echenique VC (2008a) Gene expression in diplosporous and sexual Eragrostis curvula genotypes with differing ploidy levels. Plant Mol Biol 67:11–23. doi:10.1007/s11103-008-9305-9 PubMedCrossRefGoogle Scholar
  4. Cervigni GD, Paniego N, Díaz M, Selva JP, Zappacosta D, Zanazzi D, Landerreche I, Felitti S, Pessino S, Spangenberg G, Echenique VC (2008b) Expressed sequence tag analysis and development of gene associated markers in a near-isogenic plant system of Eragrostis curvula. Plant Mol Biol 67:1–10. doi:10.1007/s11103-007-9282-4 PubMedCrossRefGoogle Scholar
  5. Chen ZJ, Ni Z (2006) Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. Bioassays 28(3):240–252. doi:10.1002/bies.20374 CrossRefGoogle Scholar
  6. Comai L, Tyagi AP, Winter K, Holmes-Davis R, Reynolds SH, Stevens Y, Byers B (2000) Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. Plant Cell 12:1551–1567PubMedCrossRefGoogle Scholar
  7. Dice LR (1945) Measures of the amount of ecologic association between species. Ecology 26:297–302. doi:10.2307/1932409 CrossRefGoogle Scholar
  8. Feldman M, Liu B, Segal G, Abbo S, Levy AA, Vega JM (1997) Rapid elimination of low-copy DNA sequences in polyploid wheat: a possible mechanism for differentiation of homoeologous chromosomes. Genetics 147:1381–1387PubMedGoogle Scholar
  9. Jaccard P (1908) Nouvelles recherches sur la ditribution florale. Bull Soc Vaud Sci Nat 44:223–270Google Scholar
  10. Kellogg EA (2003) What happens to genes in duplicated genomes. Proc Natl Acad Sci USA 100:4369–4371. doi:10.1073/pnas.0831050100 PubMedCrossRefGoogle Scholar
  11. Ma X-F, Gustafson JP (2005) Genome evolution of allopolyploids: a process of cytological and genetic diploidization. Cytogenet Genome Res 109:236–249. doi:10.1159/000082406 PubMedCrossRefGoogle Scholar
  12. Ma X-F, Fang P, Gustafson JP (2004) Polyploidization-induced genome variation in triticale. Genome 47:839–848. doi:10.1139/g04-051 PubMedCrossRefGoogle Scholar
  13. Madlung A, Masuelli R, Watson B, Reynolds S, Davison J, Comai L (2002) Re-modeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol 129:733–746. doi:10.1104/pp.003095 PubMedCrossRefGoogle Scholar
  14. Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220PubMedGoogle Scholar
  15. Martelotto LG, Ortiz JPA, Stein J, Espinoza F, Quarin CL, Pessino SC (2005) A comprehensive analysis of gene expression alterations in a newly synthesized Paspalum notatum autotetraploid. Plant Sci 169(1):211–220. doi:10.1016/j.plantsci.2005.03.015 CrossRefGoogle Scholar
  16. Martelotto LG, Ortiz JPA, Stein J, Espinoza F, Quarin CL, Pessino SC (2007) Genome variation induced by a change of the ploidy level in P. notatum. Plant Sci 172(5):970–977. doi:10.1016/j.plantsci.2007.02.001 CrossRefGoogle Scholar
  17. McClelland M, Nelson M, Raschke E (1994) Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res 22:3640–3659. doi:10.1093/nar/22.17.3640 PubMedCrossRefGoogle Scholar
  18. Mecchia MA, Ochogavía A, Selva JP, Laspina N, Felitti S, Martelotto LG, Spangenberg G, Echenique V, Pessino SC (2007) Genome polymorphisms and gene differential expression in a ‘back-and-forth’ ploidy-altered series of weeping lovegrass (Eragrostis curvula). J Plant Physiol 164(8):1051–1061. doi:10.1016/j.jplph.2006.07.002 PubMedCrossRefGoogle Scholar
  19. Murashige S, Skoog F (1962) A revised medium for rapid growth and bioassay with tobacco tissue cultures. Physiol Plant 15:473–497. doi:10.1111/j.1399-3054.1962.tb08052.x CrossRefGoogle Scholar
  20. Quarin CL, Espinoza F, Martínez EJ, Pessino SC, Bovo OA (2001) A rise of ploidy level induces the expression of apomixis in Paspalum notatum. Sex Plant Reprod 13:243–249. doi:10.1007/s004970100070 CrossRefGoogle Scholar
  21. Rangwala SH, Richards EJ (2004) The value-added genome: building and maintaining genomic cytosine methylation landscapes. Curr Opin Genet Dev 14:686–691. doi:10.1016/j.gde.2004.09.009 PubMedCrossRefGoogle Scholar
  22. Song K, Lu P, Tang K, Osborn TC (1995) Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution. Proc Natl Acad Sci USA 92:7719–7723. doi:10.1073/pnas.92.17.7719 PubMedCrossRefGoogle Scholar
  23. Spearman C (1904) The proof and measurement of association between two things. Am J Psychol 15:72–101. doi:10.2307/1412159 CrossRefGoogle Scholar
  24. Stupar RM, Bhaskar PB, Yandell BS, Rensink WA, Hart AL, Ouyang S, Veilleux RE, Busse JS, Erhardt RJ, Buell CR, Jiang J (2007) Phenotypic and transcriptomic changes associated with potato autopolyploidization. Genetics 176(4):2055–2067. doi:10.1534/genetics.107.074286 PubMedCrossRefGoogle Scholar
  25. Voigt P, Rethman N, Poverene M (2004) Lovegrasses. In: American Society of Agronomy, Crop Science Society of America, Soil Science Society of America, Warm-Season (C4) Grasses, Agronomy Monograph No. 45, chap 32, pp 1027–1056Google Scholar
  26. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Homes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA finger printing. Nucleic Acids Res 23:4407–4414. doi:10.1093/nar/23.21.4407 PubMedCrossRefGoogle Scholar
  27. Wang J, Tian L, Madlung A, Lee HS, Chen M, Lee JJ, Watson B, Kagochi T, Comai L, Chen ZJ (2004) Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids. Genetics 167:1961–1973. doi:10.1534/genetics.104.027896 PubMedCrossRefGoogle Scholar
  28. Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42:225–249. doi:10.1023/A:1006392424384 PubMedCrossRefGoogle Scholar
  29. Xiong LZ, Xu CG, Saghai Maroof MA (1999) Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by methylation-sensitive polymorphism technique. Mol Gen Genet 261:439–446. doi:10.1007/s004380050986 PubMedCrossRefGoogle Scholar
  30. Zhang X, Yazaki J, Sundaresan A, Cokus S, Chan S, Chen H, Henderson IR, Shinn P, Pellegrini M, Jacobsen SE, Ecker JR (2006) Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126:1189–1201. doi:10.1016/j.cell.2006.08.003 PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Ana C. Ochogavía
    • 1
  • Gerardo Cervigni
    • 2
  • Juan P. Selva
    • 2
  • Viviana C. Echenique
    • 2
  • Silvina C. Pessino
    • 1
  1. 1.Facultad de Ciencias AgrariasUniversidad Nacional de Rosario ArgentinaZavallaArgentina
  2. 2.Centro de Recursos Naturales de la Zona Semiárida (CERZOS CONICET)Universidad Nacional del SurBahía BlancaArgentina

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