Abstract
Sweet orange is an important group of citrus cultivars, which includes a number of bud sport cultivars. Little is known about the CpG methylation status of the CCGG sequences in the orange genome. In this study, methylation-sensitive amplification polymorphism (MSAP), based on the application of isoschizomers (Hpa II and Msp I), was first used to analyze cytosine methylation patterns in 57 orange cultivars that were not fully differentiated by regular DNA molecular markers. Three types of bands were generated from ten primer pairs. Type I bands were present following restriction with Eco RI + Hpa II and Eco RI + Msp I; type II or type III were present only following restriction with either Eco RI + Hpa II or with Eco RI + Msp I. The total number of these three types of bands was 802, 72, and 157, respectively. Among these, the number of polymorphic bands were 244 (30.2%), 23 (31.9%), and 32 (20.4%), in type I, II and III, respectively. The methylation patterns of these 57 cultivars are discussed and assessed by dendrograms derived from the analysis of polymorphic MSAP bands. The distribution of polymorphic bands of the above three types demonstrate the methylation patterns and frequency at the cytosine loci. We suggest that methylation events could be more frequent than demethylation events, and that the methylation patterns maybe associated with phenotypic traits.
Similar content being viewed by others
References
Ashikawa I (2001) Surveying CpG methylation at 5′-CCGG the genomes of rice cultivars. Plant Mol Biol 45:31–39
Baurens FC, Bonnot F, Bienvenu D, Causse S, Legavre T (2003) Using SD-AFLP and MSAP to assess CCGG methylation in the banana genome. Plant Mol Biol Rep 21:339–348
Bretò MP, Ruitz C, Pina JA, Asín MJ (2001) The diversification of Citrus clementina Hort. Ex Tan., a vegetatively propagated crop species. Mol Phylogenet Evol 21:285–293
Cameron JW, Frost HB (1968) Genetics, breeding and nucellar embryony. In: Reuthen W, Webber HJ, Batchelor LD (eds) The citrus industry, vol 2. University of California Press, Berkeley, CA, pp 325–370
Cervera MT, Ruíz-Garcia L, Martínez-Zapater JM (2002) Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. Mol Gen Genomics 268:543–552
Debasis C, Yu KW, Paek KY (2003) Detection of DNA methylation changes during somatic embryogenesis of Siberian ginseng (Eleuterococcus senticosus). Plant Sci 165:61–68
Fang J, Chao CT (2007) Methylation-sensitive amplification polymorphism in date palms (Phoenix dactylifera L.) and their off-shoots. Plant Biol 9:526–533
Fang DQ, Roose ML (1997) Identification of closely related Citrus cultivars with inter-simple sequence repeat markers. Theor Appl Genet 95:408–417
Fang J, Wang C, Yu H, Zheng Y, Li X, Song C, Chen J (2009) Identification of 57 navel sweet orange cultivars with AFLP markers. J Hortic Sci Biotechnol 84:585–590
Federici CT, Fang DQ, Scora RW, Roose ML (1998) Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theor Appl Genet 96:812–822
Felsenstein J (1993) PHYLIP (Phylogenetic Inference Package) Version 3.5c (http://cmgm.stanford.edu/phylip/). Department of Genetics, University of Washington, Seattle, WA, USA
Ferguson-Smith AC, Surani MA (2001) Imprinting and the epigenetic asymmetry between parental genomes. Science 293:1086–1089
Finnegan EJ (2001) Is plant gene expression regulated globally? Trends Genet 17:361–365
Finnegan EJ, Peacock WJ, Dennis ES (2000) DNA methylation, a key regulator of plant development and other processes. Curr Opin Genet Dev 10:217–223
Hafiz IA, Anjum MA, Grewal AG, Chaudhary GA (2001) DNA methylation—an essential mechanism in plant molecular biology. Acta Physiol Plant 23:491–499
Herrero R, Asins MJ, Carbonell EA, Navrro L (1996) Genetic diversity in the orange subfamily Aurantoideae. I. Interspecies and intragenus genetic variability. Theor Appl Genet 92:599–609
Hodgson RW (1967) Horticultural varieties of citrus, vol 1. Reuthen W, Webber HJ, Batchelor LD (eds) University of California Press, Berkeley, CA, USA, pp 431–591
Jaligot E, Beulé T, Baurens F-C, Billotte N, RIVAL A (2004) Search for methylation-sensitive amplification polymorphisms associated with the “mantled” variant phenotype in oil palm (Elaeis guineensis Jacq.). Genome 47:224–228
Jeddeloh JA, Richards EJ (1996) mCCG methylation in angiosperms. Plant J 9:579–586
Kahn TL, Bier OJ, Beaver RJ (2007) New late-season navel orange varieties evaluated for quality characteristics. Calif Agric 61:138–143
Kalisz S, Purugganan MD (2004) Epialleles via DNA methylation: consequences for plant evolution. Trends Ecol Evol 19:309–314
Kovarik A, Matyasck R, Lcitch A, Gazdova B, Fulnccek J, Bezdek M (1997) Variability in CpNpG methylation in higher plant genomes. Gene 204:25–33
Law RD, Suttle JC (2002) Transient decrease in methylation at 5′-CCGG-3′ sequences in potato (Solanum tuberosum) meristem DNA during progression of tubers through dormancy precede the resumption of sprout growth. Plant Mol Biol 51:437–447
Li X, Xu M, Korban SS (2002) DNA methylation profiles differ between field- and in vitro-grown leaves of apple. J Plant Physiol 159:1229–1234
Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129
Manning K, Tör M, Poole M, Hong Y, Thompson AJ, King GJ, Giovannoni JJ, Seymour GB (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38:948–952
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
Messeguer R, Ganal MW, Steffens JC, Tanksley SD (1991) Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA. Plant Mol Biol 16:753–770
Pradhan S, Adams LP (1995) Distinct CG and CNG DNA methyltransferases in Pisum sativum. Plant J 7:471–481
Rapp RA, Wendel JF (2005) Epigenetics and plant evolution. New Phytol 168:81–91
Rohlf FJ (2000) NTSYS pc, numerical taxonomy and multivariate analysis system. Version 2.1 user guide. Exeter Software Publ, Setauket, NY
Silva AJ, White R (1988) Inheritance of allelic blueprints for methylation patterns. Cell 54:145–152
Sneath PHA, Sokal RR (1973) Numerical taxonomy: the principles and practice of numerical classification. W.H. Freeman, San Francisco, CA
Wolffe AP, Matzke MA (1999) Epigenetics: regulation through repression. Science 286:481–486
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by L. A. Kleczkowski.
Rights and permissions
About this article
Cite this article
Fang, JG., Song, CN., Qian, JL. et al. Variation of cytosine methylation in 57 sweet orange cultivars. Acta Physiol Plant 32, 1023–1030 (2010). https://doi.org/10.1007/s11738-010-0491-0
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11738-010-0491-0