Fig. 5

Transgenerational DMRs correlate with expression levels of epigenes. a, b Seedling phenotypes (a) and aboveground dry weight (b) at the same stage in Mo17 and BM6S3 (left), B73 and MB6S3 (middle), and MB and BM hybrids (right). Photos were taken at the same time with the same scale (bars = 10 mm). Double asterisks indicate statistical significance (P < 0.05 and n = 16 replicates, two-tailed Student’s t-test). c Principal component analysis (PCA) of transcriptome variation among six lines with the overall variance explained by PC1 (x-axis) and PC2 (y-axis). d Positive correlation (r = Pearson’s correlation coefficient) of expression level changes of 43 epigenes in MB6S3/B73 (x-axis) with those in Mo17/B73 (y-axis). e Positive correlation (r = Pearson’s correlation coefficient) of expression level changes of 57 epigenes in BM6S3/Mo17 (x-axis) with those in in B73/Mo17 (y-axis). f Gene Ontology (GO) overrepresentation of 97 tgDMRs-associated genes in MB6S3 and BM6S3 lines (P < 0.05 and fold enrichment > = 2.5). g An example of the epigene (Zm00001d026577), showing location of DTA transposon, mRNA, siRNA, and CHH methylation levels in Mo17, B73, MB6S3, and MB lines. Scales shown are 0–1 (CHH methylation), 0–100 (siRNA), and 0–10 (mRNA). Numbers indicate average methylation levels of DMR methylation, siRNA expression (RPTM), and gene expression (FPKM). Double asterisks indicate statistically significant changes between MB hybrid and MPV or between MB6S3 and its recurrent parent B73 (P < 0.05, one-way ANOVA test for methylation; two-tailed Student’s t-test for siRNA and gene expression)