Analysis of sulphur and chlorine induced DNA cytosine methylation alterations in fresh corn (Zea mays L. saccharata and rugosa) leaf tissues by methylation sensitive amplification polymorphism (MSAP) approach

Abstract

DNA (cytosine) methylation mechanism is another way through which plants respond to various cues including soil fertility amendments and abiotic stresses, and the mechanism has been used to infer some physiological, biochemical or adaptation processes. Despite numerous studies on global DNA methylation profiling in various crop species, however, researches on fresh corn (Zea mays L. saccharata or rugosa) remain largely unreported. The study aimed at investigating sulphur and chlorine induced DNA methylation changes in the fresh corn leaves of field-grown plants at the milk stage. Methylation sensitive amplification polymorphism (MSAP) technique was used to profile sulphur (S) and chlorine (Cl) induced DNA methylation patterns, levels and polymorphism alterations at the CCGG sites in fresh corn leaves of TDN21, JKN2000 and JKN928 hybrid cultivars. Twelve primer pairs used effectively detected 325 MSAP bands, exhibiting differentially methylated sites in the genomic DNA of all the three cultivars, with control showing higher (48.9-56.3%) type I bands as compared to sulphur (34.8-44.9%) and chlorine (40.9-47.4%) treatment samples. Consequently, total methylation levels were greater in S and Cl treatment samples than control; accounting for 43.7-59.7, 51.1-65.2 and 46.8-55.1% of total sites in TDN21, JKN2000 and JKN928, respectively. Full methylation of the internal cytosine was greater than hemi-methylation. Further, demethylation polymorphic loci significantly exceeded methylation polymorphic loci, being greater in S than Cl and control samples in all cultivars. Sulphur and chlorine have a profound influence on DNA methylation patterns and levels at the milk stage, principally by increasing the demethylation loci in the internal cytosine of the fresh corn genome. We speculate that these methylation alterations play an integral role in photosynthates assimilation and physiochemical pathways regulating quality parameters in kernels, as well as abiotic stress responses in fresh corn.

Exploring the crop epigenome: a comparison of DNA methylation profiling techniques

“…Versatility of this method, regardless of the genome size or the presence of a reference genome ( Chwialkowska et al., 2017 ), makes it widely applicable in both model and non-model plants. In Arabidopsis , MSAP has been used to detect stress-induced methylation changes, such as cryopreservation ( Wang and He, 2009 ), cadmium stress ( Li et al., 2015b ) and sulfur dioxide stress ( Yi and Li, 2013 ), also in crops, such as faba bean under dehydration ( Abid et al., 2017 ), Sesamum indicum under drought and waterlogging ( Komivi et al., 2018 ), and maize under sulfur and chlorine stress ( Zenda et al., 2018 ). Additionally, differences in cytosine methylation between Pinus pinea individuals and populations, and Laguncularia racemosa populations have been studied ( Lira-Medeiros et al., 2010 ; Saez-Laguna et al., 2014 ).…”

Physiological, Biochemical, and Epigenetic Reaction of Maize (Zea mays L.) to Cultivation in Conditions of Varying Soil Salinity and Foliar Application of Silicon

“…In recent years, considerable attention has been focused on the role of Si in increasing plant resistance to biotic and abiotic stress factors [ 15 , 30 , 31 , 32 , 33 , 34 ]. Some researchers consider Si to be a quasi-essential element [ 35 ].…”

“…The positive effects of the presence of Si are demonstrable mainly under different stress conditions and when the Si concentration in plant tissues is high [ 28 , 36 , 37 ]. Supplying plants with soluble and easily assimilable Si compounds may, therefore, be one of the important methods in reducing the negative effects of environmental stress factors [ 1 , 29 , 35 , 38 , 39 ].…”