Genome-wide DNA methylation analysis and biochemical response provide insights into the initial domestication of halophyte Puccinellia tenuiflora

Domestication of the halophytes with economic values will promise hope to deal with soil salinization problem. We domesticated a wild extreme halophyte Puccinellia tenuiflora individual for two years by growing it under non-saline condition in a greenhouse. We conducted genome-wide DNA methylation analysis, transcriptome analysis and biochemical measurements to uncover mechanisms underlying the salinity tolerance alteration of P. tenuiflora induced by the non-saline domestication. Our results showed that the non-saline domestication induced methylation status alteration of a number of genes and transposable elements (TEs), with much higher frequency of hypomethylation than that of hypermethylation. The DNA methylation modifications were observed in many key metabolism genes and crucial salinity tolerant genes. Particularly, the non-saline domestication induced hypomethylation of promoter regions of 21 E3 ubiquitin-protein ligase genes and 6 nitrogen metabolism genes, indicating that DNA methylation status of E3 ubiquitin-protein ligase genes and nitrogen metabolism genes are domestication-impressionable. We assessed whether the non-saline domestication can change the salinity tolerance of P. tenuiflora. The results showed that non-saline domesticated plants showed weakened salinity tolerance, which may be attributable to altered metabolic characteristics. DNA methylation and TE may be integrated into an environment-sensitive molecular engine that promotes rapid domestication of P. tenuiflora.