Transgenerational Variations in DNA Methylation Induced by Drought Stress in Two Rice Varieties with Distinguished Difference to Drought Resistance

<div><p>Adverse environmental conditions have large impacts on plant growth and crop production. One of the crucial mechanisms that plants use in variable and stressful natural environments is gene expression modulation through epigenetic modification. In this study, two rice varieties with different drought resistance levels were cultivated under drought stress from tilling stage to seed filling stage for six successive generations. The variations in DNA methylation of the original generation (G0) and the sixth generation (G6) of these two varieties in normal condition (CK) and under drought stress (DT) at seedling stage were assessed by using Methylation Sensitive Amplification Polymorphism (MSAP) method. The results revealed that drought stress had a cumulative effect on the DNA methylation pattern of both varieties, but these two varieties had different responses to drought stress in DNA methylation. The DNA methylation levels of II-32B (sensitive) and Huhan-3 (resistant) were around 39% and 32%, respectively. Genome-wide DNA methylation variations among generations or treatments accounted for around 13.1% of total MSAP loci in II-32B, but was only approximately 1.3% in Huhan-3. In II-32B, 27.6% of total differentially methylated loci (DML) were directly induced by drought stress and 3.2% of total DML stably transmitted their changed DNA methylation status to the next generation. In Huhan-3, the numbers were 48.8% and 29.8%, respectively. Therefore, entrainment had greater effect on Huhan-3 than on II-32B. Sequence analysis revealed that the DML were widely distributed on all 12 rice chromosomes and that it mainly occurred on the gene’s promoter and exon region. Some genes with DML respond to environmental stresses. The inheritance of epigenetic variations induced by drought stress may provide a new way to develop drought resistant rice varieties.</p> </div

Distribution of the DML at chromosome level (A) and gene level (B)c.

<p>Distribution of the DML at chromosome level (A) and gene level (B)c.</p

Expression of genes with DML.

<div><p>(A) Expression of genes which re-methylated in CK vs. DT in G0 of II-32B;</p> <p>(B) Expression of genes which re-methylated in CK vs. DT in G0 of Huhan-3;</p> <p>(C) Expression of genes which de-methylated in CK vs. DT in G0 of II-32B;</p> <p>(D) Expression of genes which de-methylated in CK vs. DT in G0 of Huhan-3.</p></div

Selective amplification with primer-pair of E09/HM39 for five digestion sets of both varieties.

<p>Selective amplification with primer-pair of E09/HM39 for five digestion sets of both varieties.</p

Further analysis of DNA methylation variations between generations and between treatments.

<p>(A) Comparison based on generations (G0 and G6). Only G0 means that DNA methylation variations occurred between CK and DT in G0, but not in G6; Both G0 and G6 means that DNA methylation variations occurred between CK and DT in both G0 and G6; Only G6 means that DNA methylation variations occurred between CK and DT in G6, but not at G0; Non means that no DNA methylation variations occurred between CK and DT in both G0 and G6, but G0 and G6 had different methylation pattern. (B) Comparison based on treatments (CK and DT). Only CK means that DNA methylation variations occurred between G0 and G6 under CK, but not under DT; Both CK and DT means that DNA methylation variations occurred between G0 and G6 under both CK and DT; Only DT means DNA methylation variations occurred between G0 and G6 under DT, but not under CK; Non means no DNA methylation variations occurred between G0 and G6 under both CK and DT, but CK and DT had different methylation pattern.</p