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. 2021 May 10;10(5):946.
doi: 10.3390/plants10050946.

Differential Methylation Patterns in Apomictic vs. Sexual Genotypes of the Diplosporous Grass Eragrostis curvula

Jose Carballo  1   2 , Diego Zappacosta  1   2 , Gianpiero Marconi  3 , Jimena Gallardo  1   2 , Marco Di Marsico  3 , Cristian A Gallo  1 , Mario Caccamo  4 , Emidio Albertini  3 , Viviana Echenique  1   2
Affiliations

Differential Methylation Patterns in Apomictic vs. Sexual Genotypes of the Diplosporous Grass Eragrostis curvula

Jose Carballo et al. Plants (Basel). .

Abstract

DNA methylation is an epigenetic mechanism by which a methyl group is added to a cytosine or an adenine. When located in a gene/regulatory sequence it may repress or de-repress genes, depending on the context and species. Eragrostis curvula is an apomictic grass in which facultative genotypes increases the frequency of sexual pistils triggered by epigenetic mechanisms. The aim of the present study was to look for correlations between the reproductive mode and specific methylated genes or genomic regions. To do so, plants with contrasting reproductive modes were investigated through MCSeEd (Methylation Context Sensitive Enzyme ddRad) showing higher levels of DNA methylation in apomictic genotypes. Moreover, an increased proportion of differentially methylated positions over the regulatory regions were observed, suggesting its possible role in regulation of gene expression. Interestingly, the methylation pathway was also found to be self-regulated since two of the main genes (ROS1 and ROS4), involved in de-methylation, were found differentially methylated between genotypes with different reproductive behavior. Moreover, this work allowed us to detect several genes regulated by methylation that were previously found as differentially expressed in the comparisons between apomictic and sexual genotypes, linking DNA methylation to differences in reproductive mode.

Keywords: DNA methylation; apomixis; diplospory; epigenetics; eragrostis.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Relative methylation frequencies of the loci contained in each DMR identified from the comparison between the facultative apomictic or sexual (A), full apomictic or sexual (B) and facultative or full apomictic (C) plants. Sex: sexual plants, Fac: facultative apomictic plants, Full: full apomictic plants. Lower levels of relative methylation are indicated by more intense red color while higher levels of relative methylation are indicated by complete yellow.
Figure 2
Figure 2
Number of DMRs overlapping genomic regions (X axis) in the Facultative vs. Sexual (A), Full Apomictic vs. Sexual (B) and Full Apomictic vs. Facultative (C) comparisons.
Figure 3
Figure 3
Differentially methylated positions along the EGBs for CG, CHG, CHH, and 6mA contexts. X axis correspond to 2000 bp before and after the ATG and STOP codon respectively.
Figure 4
Figure 4
Venn diagram showing the de-methylated (A) and methylated (B) genes specific and shared between the full and facultative apomictic genotypes compared with the sexual one.
Figure 5
Figure 5
ROS1 and ROS4 genomic regions, showing 2000 bp before and after the start and stop codon, respectively. Blue rectangles represent DMRs, red rectangles exons and green rectangles UTR.
Figure 6
Figure 6
Differentially enriched GO terms considering de-methylated and methylated genes in the AVS (A,B), FVS (C,D), and AVF (E,F) comparisons.
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