Abstract
DNA methylation is known as an epigenetic modification that affects gene expression in plants. Variation in CpG methylation behavior was studied in two natural horse gram (Macrotyloma uniflorum [Lam.] Verdc.) genotypes, HPKC2 (drought-sensitive) and HPK4 (drought-tolerant). The methylation pattern in both genotypes was studied through methylation-sensitive amplified polymorphism. The results revealed that methylation was higher in HPKC2 (10.1%) than in HPK4 (8.6%). Sequencing demonstrated sequence homology with the DRE binding factor (cbf1), the POZ/BTB protein, and the Ty1-copia retrotransposon among some of the polymorphic fragments showing alteration in methylation behavior. Differences in DNA methylation patterns could explain the differential drought tolerance and the epigenetic signature of these two horse gram genotypes.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Alina R, Sgorbati S, Santagostino A, Labra M, Ghiani A, Citterio S (2004) Specific hypomethylation of DNA is induced by heavy metals in white clover and industrial hemp. Physiol Plant 121:472–480
Aravind L, Koonin EV (1999) Fold prediction and evolutionary analysis of the POZ domain: structural and evolutionary relationship with the potassium channel tetramerization domain. J Mol Biol 285:1353–1361
Bhardwaj J, Yadav SK (2012) Comparative study on biochemical parameters and antioxidant enzymes in a drought-tolerant and a sensitive variety of horsegram (Macrotyloma uniflorum) under drought stress. Am J Plant Physiol 7:17–29
Bolbhat SN, Dhumal KN (2009) Induced macromutations in horsegram [Macrotyloma uniflorum (Lam.) Verdc.]. Legume Res 32:278–281
Boyko A, Kovalchuk I (2008) Epigenetic control of plant stress response. Environ Mol Mutagen 49:61–72
Capitao C, Paiva JAP, Santos DM, Fevereiro P (2011) In Medicago truncatula, water deficit modulates the transcript accumulation of components of small RNA pathways. BMC Plant Biol 11:79
Cervera M, Ruiz-García L, Martínez-Zapater J (2002) Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. Mol Genet Genomics 268:543–552
Chan SWL, Henderson IR, Jacobsen SE (2005) Gardening the genome: DNA methylation in Arabidopsis thaliana. Nat Rev Genet 6:351–360
Cheng C, Daigen M, Hirochika H (2006) Epigenetic regulation of the rice retrotransposon Tos17. Mol Genet Genomics 276:378–390
Choi CS, Sano H (2007) Abiotic-stress induces demethylation and transcriptional activation of a gene encoding a glycerophosphodiesterase-like protein in tobacco plants. Mol Genet Genomics 277:589–600
Collins T, Stone JR, Williams AJ (2001) All in the family: the BTB/POZ, KRAB, and SCAN domains. Mol Cell Biol 21:3609–3615
Courtier B, Heard E, Avner P (1995) Xce haplotypes show modified methylation in a region of the active X chromosome lying 3′ to Xist. Proc Natl Acad Sci USA 92:3531–3535
Dyban AP, Dyban PA (2006) Theoretical and applied aspects of epigenetic reprogramming in mammalian development. Russ J Genet 42:1362–1366
Fang JG, Chao CT (2006) Methylation-sensitive amplification polymorphism in date palms (Phoenix dactylifera L.) and their off-shoots. Plant Biol 9:526–533
Finnegan EJ, Peacock WJ, Dennis ES (1996) Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development. Proc Natl Sci USA 93:8449–8454
Jaligot E, Beul T, Baurens F, 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
Keyte A, Percifield R, Liu B, Wendel J (2006) Infraspecific DNA methylation polymorphism in cotton (Gossypium hirsutum L.). J Hered 97:444–450
Koukalova B, Fojtova M, Lim KY, Fulnecek J, Leitch AR, Kovarik A (2005) Dedifferentiation of tobacco cells is associated with ribosomal RNA gene hypomethylation, increased transcription, and chromatin alterations. Plant Physiol 139:275–286
Li XL, Yu XM, Wang NN, Feng QZ, Dong ZY, Liu LX, Shen JL, Liu B (2007) Genetic and epigenetic instabilities induced by tissue culture in wild barley (Hordeum brevisubulatum (Trin) Link). Plant Cell Tissue Organ C 90:153–168
Madlung A, Masuelli RW, Watson B, Reynolds SH, Davison J, Comai L (2002) Remodeling of DNA methylation and phenotypic and transcriptional changes in synthetic Arabidopsis allotetraploids. Plant Physiol 129:733–746
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
Novillo F, Alonso JM, Ecker JR, Salinas J (2004) CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis. Proc Natl Acad Sci USA 16:3985–3990
Platonov ES, Isaev DA (2006) Genomic imprinting in epigenetic of mammals. Russ J Genet 42:1030–1042
Richards EJ (1997) DNA methylation and plant development. Trends Genet 13:319–323
Salmon A, Clotault J, Jenczewski E, Chable V, Manzanares-Dauleux M (2008) Brassica oleracea displays a high level of DNA methylation polymorphism. Plant Sci 174:61–70
Sasaki H, Matsui Y (2008) Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat Rev Genet 9:129–140
Schellenbaum P, Mohler V, Wenzel G, Walter B (2008) Variation in DNA methylation patterns of grapevine somaclones (Vitis vinifera L.). BMC Plant Biol 8:78–87
Sjakste NI, Sjakste TG (2007) Possible involvement of DNA breaks in epigenetic regulation of cell differentiation. Russ J Genet 43:467–484
Takeda S, Paszkowski J (2006) DNA methylation and epigenetic inheritance during plant gametogenesis. Chromosoma 115:27–35
Tan MP (2010) Analysis of DNA methylation of maize in response to osmotic and salt stress based on methylation-sensitive amplified polymorphism. Plant Physiol Biochem 48:21–26
Tran R, Henikoff J, Zilberman D, Ditt R, Jacobsen S, Henikoff S (2005) DNA profiling identifies CG methylation clusters in Arabidopsis genes. Curr Biol 15:154–159
Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acid Res 23:4407–4414
Wang WS, Pan YJ, Zhao XQ, Dwivedi D, Zhu LH, Ali J, Fu BY, Li ZK (2010) Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.). J Exp Bot. doi:10.1093/jxb/erq391
Weinhold B (2006) Epigenetics: the science of change. Environ Health Perspect 114:160–167
Xiao WY, Custard KD, Brown RC, Lemmon BE, Harada JJ, Goldberg RB, Fischer RL (2006) DNA methylation is critical for Arabidopsis embryogenesis and seed viability. Plant Cell 18:805–814
Xiong L, Xu C, Saghai-Maroof M, Zhang Q (1999) Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique. Mol Genet Genomics 261:439–446
Zhang L, Yang G, Liu P, Hong D, Li S, He Q (2011) Genetic and correlation analysis of silique-traits in Brassica napus L. by quantitative trait locus mapping. Theor Appl Genet 122:21–31
Acknowledgments
The authors are thankful to the Director, CSIR-IHBT, for his continuous encouragement and support. Dr. R. K. Chahota, Department of Plant Breeding and Genetics, CSK HPKV, Palampur, is duly acknowledged for providing horse gram seeds. This work was supported by grants from CSIR, GOI, to S. K. Yadav as a CSIR-YSA project (IHBT communication No. 3426).
Author information
Authors and Affiliations
Corresponding author
Additional information
J. Bhardwaj and M. Mahajan contributed equally to this study.
Rights and permissions
About this article
Cite this article
Bhardwaj, J., Mahajan, M. & Yadav, S.K. Comparative Analysis of DNA Methylation Polymorphism in Drought Sensitive (HPKC2) and Tolerant (HPK4) Genotypes of Horse Gram (Macrotyloma uniflorum). Biochem Genet 51, 493–502 (2013). https://doi.org/10.1007/s10528-013-9580-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10528-013-9580-2