Fig. 2

Differentially methylated region (DMR) detection and comparison to DNA sequence regions under selection (DSRs). a DMRs detected in soybean domestication and improvement. b Genome-wide distributions of DMRs and DSRs. c Genomic compositions of DMRs and DSRs. TE regions were defined as regions masked by RepeatMasker using soybean annotated TEs as the library. d Length comparison between DMRs and DSRs. ***p < 0.001 by ANOVA. e Genetic diversity comparisons between DMRs, DSRs, and non-selected regions (NSRs) from different genomic regions. ANOVA were performed for each genomic region. Different letters at the top of each column indicate significant differences by ANOVA (p < 0.001). f Genetic diversity comparisons between high methylation variation windows (MVWs) and low methylation variation windows for different genomic regions. ***p < 0.001 by t-test