Differential epigenetic marks are associated with apospory expressivity in diploid Paspalum rufum

Apomixis seems to emerge from deregulation of pre-existing genes involved in sexuality, by genetic and/or epigenetic mechanisms. The trait is associated with polyploidy, but diploid individuals of Paspalum rufum can form aposporous embryo sacs and develop clonal seeds. Moreover, diploid hybrid families presented wide apospory expressivity variation. To locate methylation changes associated with apomixis expressivity, we compare relative DNA methylation levels, at CG, CHG, and CHH contexts, between full-sib P. rufum diploid genotypes presenting differential apospory expressivity. The survey was performed by Methylation content sensitive enzyme ddRAD (MCSeEd) strategy on samples at premeiosis/meiosis and postmeiosis stages. Principal component analysis and heatmaps, based on the relative methylation level, clearly discriminate samples with contrasting apospory-expressivity. Differential methylated contigs (DMCs) showed 14% of homology to known transcripts of Paspalum notatum reproductive transcriptome and almost half of them were also differentially expressed between apomictic and sexual samples. DMC showed homology to genes involved in flower growth, development, and apomixis. Moreover, a high proportion of DMCs aligned on genomic regions associated with apomixis in Setaria italica. Several stage-specific differential methylated sequences were identified as associated to apospory expressivity which would guide future functional gene characterization, in relation to apomixis success at diploid and tetraploid level.