Root-Specific DNA Methylation in Chloris virgata, a Natural Alkaline-Resistant Halophyte, in Response to Salt and Alkaline Stresses

DNA methylation has long been considered to play important roles in the regulation of plant response to multiple environmental stresses. As it is with saline soils, alkaline soils are important agricultural contaminants that have complex effects on plant metabolism and, in particular, on root physiology. However, there are no reports on epigenetic responses of plants to both salt and alkaline stresses. In this study, we report on the effects of salt stress (S, 1:1 molar ratio of NaCl to Na2SO4) as well as alkaline stress (A, 1:1 molar ratio of NaHCO3 to Na2CO3) on DNA methylation in an alkaline-resistant halophyte, Chloris virgate. A total of 959 and 1,040 DNA fragments were amplified in leaves and roots, respectively, by using 21 pairs of selective primers in methylation-sensitive amplified polymorphism analysis. The results showed that the overall level of methylation in leaves was 18.35%, and in roots, it was 12.40%. Furthermore, both salt and alkaline stress caused DNA methylation variations, predominantly in the roots. The variation ratio was 0.75% in leaves and 5.29% in roots under salt stress and 1.26% in leaves and 14.17% in roots under alkaline stress. The results suggested that alkaline stress was more destructive and complex than salt stress and that the DNA methylation regulation that occurred in the roots might play an important role in the acquirement and inheritance of salt and alkaline stress tolerance.