Estimation of genomic instability and DNA methylation due to aluminum (Al) stress in wheat (Triticum aestivum L.) using iPBS and CRED-iPBS analyses

Aluminum (Al) toxicity is a serious factor restricting crop productivity in acid soil, and Al is the major cause of phytotoxicity.However, the role of Al toxicity in interprimer binding site (iPBS) polymorphism, genomic instability, and DNA methylation has notbeen fully investigated. In the current study, the effects of different Al concentrations on iPBS polymorphism, genomic instability, andDNA methylation were investigated in seedlings of three wheat cultivars: Haymana 79, Kılçıksız, and Bezostaja 1. A higher aluminumconcentration increased the polymorphism rate of the iPBS profile, but decreased genomic template stability in all cultivars. A higherAl concentration was found to cause DNA methylation. Furthermore, the coupled restriction enzyme digestion-iPBS technique wasused to detect DNA cytosine methylation level, which could help in understanding the epigenetic mechanism. The occurrence ofhypermethylation and hypomethylation was observed with respect to Al stress treatment, and Al was found to cause DNA methylation.Polymorphism in the CRED-iPBS profile and DNA methylation can be correlated to evaluate epigenetic changes under stress.

PDF

___

Andeden EE, Baloch FS, Derya M, Kilian B, Özkan H (2013). iPBSretrotransposons-based genetic diversity and relationship among wild annual Cicer species. J Plant Biochem Biot 22: 453- 466.
Anioł A (1995). Physiological aspects of aluminium tolerance associated with the long arm of chromosome 2D of the wheat (Triticum aestivum L.) genome. Theor Appl Genet 91: 510-516.
Bianchi-Hall CM, Carter TE, Bailey MA, Mian MAR, Rufty TW, Ashley DA, Parrott, WA (2000). Aluminum tolerance associated with quantitative trait loci derived from soybean PI 416937 in hydroponics. Crop Sci 40: 538-545.
Bot A, Nachtergaele F, Young A (2000). Land resource potential and constraints at regional and country levels. FAO Food and Nutrition Paper, Vol. 90. Cadet J, Douki T, Ravanat JL (2015). Oxidatively generated damage to cellular DNA by UVB and UVA radiation. J Photoch Photobio B 91: 140-155.
Cheng TF, Choudhuri S, Muldoon‐Jacobs K (2012). Epigenetic targets of some toxicologically relevant metals: a review of the literature. J Appl Toxicol 32: 643-653.
Delhaize E, Hebb DM, Richards KD, Lin JM, Ryan PR, Gardner RC (1999). Cloning and expression of a wheat (Triticum aestivum L.) phosphatidylserine synthase cDNA overexpression in plants alters the composition of phospholipids. J Biol Chem 274: 7082-7088.
Doncheva S, Amenós M, Poschenrieder C, Barceló J (2005). Root cell patterning: a primary target for aluminium toxicity in maize. J Exp Bot 56: 1213-1220.
Drewell RA, Bush EC, Remnant EJ, Wong GT, Beeler SM, Stringham JL, Oldroyd BP (2014). The dynamic DNA methylation cycle from egg to sperm in the honey bee Apis mellifera. Development 141: 2702-2711.
Erturk FA, Agar G, Arslan E, Nardemir G (2015a). Analysis of genetic and epigenetic effects of maize seeds in response to heavy metal (Zn) stress. Environ Sci Pollut R 22: 10291-10297.
Erturk FA, Aydin M, Sigmaz B, Taspinar MS, Arslan E, Agar G, Yagci S (2015b). Effects of As2 O3 on DNA methylation, genomic instability, and LTR retrotransposon polymorphism in Zea mays. Environ Sci Pollut R 22: 18601-18606.
Erturk FA, Agar G, Arslan E, Nardemir G, Sahin Z (2014a). Determination of genomic instability and DNA methylation effects of Cr on maize (Zea mays L.) using RAPD and CRED-RA analysis. Acta Physiol Plant 36: 1529-1537.
Erturk FA, Agar G, Arslan E, Nardemir G, Aydin M, Taspinar MS (2014b). Effects of lead sulfate on genetic and epigenetic changes and endogenous hormone levels in corn (Zeamays L.). Pol J Environ Stud 23: 1925-1932.
Ezaki B, Koyanagi M, Gardner R, Matsumoto H (1997). Nucleotide sequence of a cDNA for GDP dissociation inhibitor (GDI) which is induced by aluminum (Al) ion stress in tobacco cell culture. Plant Physiol 115: 314-314.
Gavery MR, Roberts SB (2010). DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas). BMC Genomics 11: 483.
Ince AG, Karaca M (2016). Association between cytosine methylation and tissue specific expression of microsatellites. FEBS J 283: 334-335.
Kalendar R, Antonius K, Smýkal P, Schulman AH (2010). iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theor Appl Genet 121: 1419-1430.
Karaca M, Ince AG, Uygur-Gocer E, Aydin A (2016). Exonic and intronic DNA methylation differences in a fiber specific gene of Pima cotton (Gossypium barbadense L.). Journal of Scientific and Engineering Research 3: 478-486.
Kochian LV (1995). Cellular mechanisms of aluminum toxicity and resistance in plants. Annu Rev Plant Biol 46: 237-260.
Kumar S, Beena AS, Awana M, Singh A (2017a). Physiological, biochemical, epigenetic and molecular analyses of wheat (Triticum aestivum L.) genotypes with contrasting salt tolerance. Front Plant Sci 8: 1-20.
Kumar S, Beena AS, Awana M, Singh A (2017b). Salt-induced tissue-specific cytosine methylation downregulates expression of HKT genes in contrasting wheat (Triticum aestivum L.) genotypes. DNA Cell Biol 36: 283-394.
Kumar S, Singh AK, Mohapatra T (2017c). Epigenetics: history, present status and future perspective. Indian J Genet Pl Br 77: 445- 463.
Laird PW (2010). Principles and challenges of genome-wide DNA methylation analysis. Nat Rev Genet 11: 191-203.
Li Y, Kumar S, Qian W (2018). Regulation of plant development by active DNA demethylation. Plant Cell Rep 37: 77-85.
Ma JF, Shen R, Nagao S, Tanimoto E (2004). Aluminum targets elongating cells by reducing cell wall extensibility in wheat roots. Plant Cell Physiol 45: 583-589.
Marfil CF, Camadro EL, Masuelli RW (2009). Phenotypic instability and epigenetic variability in a diploid potato of hybrid origin, Solanum ruiz-lealii. BMC Plant Biol 9: 21.
Mehta A, Haber JE (2014). Sources of DNA double-strand breaks and models of recombinational DNA repair. CSH Perspect Biol 6: a016428.
Meriga B, Reddy BK, Rao KR, Reddy LA, Kishor PK (2004). Aluminium-induced production of oxygen radicals, lipid peroxidation and DNA damage in seedlings of rice (Oryza sativa). J Plant Physiol 161: 63-68.
Mossor-Pietraszewska T (2001). Effect of aluminium on plant growth and metabolism. Acta Biochim Pol 48: 673-686.
Mugal CF, Ellegren H (2011). Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content. Genome Biol 12: R58.
Nardemir G, Agar G, Arslan E, Erturk FA (2015). Determination of genetic and epigenetic effects of glyphosate on Triticum aestivum with RAPD and CRED-RA techniques. Theor Exp Plant Phys 27: 131-139.
Nemli S, Kianoosh T, Tanyolac MB (2015). Genetic diversity and population structure of common bean (Phaseolus vulgaris L.) accessions through retrotransposon-based interprimer binding sites (iPBSs) markers. Turk J Agric For 39: 940-948.
Nguyen V, Burow M, Nguyen H, Le B, Le T, Paterson A (2001). Molecular mapping of genes conferring aluminum tolerance in rice (Oryza sativa L.). Theor Appl Genet 102: 1002-1010.
Sharma P, Jha AB, Dubey RS, Pessarakli M (2012). Reactive oxygen species, oxidative damage, and antioxidative defense mechanism in plants under stressful conditions. Journal of Botany 32: 243-247.
Sharma V, Collins LB, Clement JM, Zhang Z, Nakamura J, Swenberg JA (2014). Molecular dosimetry of endogenous and exogenous O6-Methyl-dG and N7-Methyl-G adducts following low dose [D3
]-methylnitrosourea exposures in cultured human cells. Chem Res Toxicol 27: 480-482.
Sigmaz B, Agar G, Arslan E, Aydin M, Taspinar MS (2015). The role of putrescine against the long terminal repeat (LTR) retrotransposon polymorphisms induced by salinity stress in Triticum aestivum. Acta Physiol Plant 37: 251.
Singer MJ, Munns DN (2006). Soils: An Introduction. Upper Saddle River, NJ, USA.
Steward N, Ito M, Yamaguchi Y, Koizumi N, Sano H (2002). Periodic DNA methylation in maize nucleosomes and demethylation by environmental stress. J Biol Chem 277: 37741-37746.
Zeinalzadehtabrizi H, Hosseinpour A, Aydin M, Haliloglu K (2015). A modified genomic DNA extraction method from leaves of sunflower for PCR based analyzes. Journal of Biodiversity and Environmental Sciences 7: 222-225.