In addition to genetic variation, epigenetic variation plays an important role in determining various biological processes. The importance of natural genetic variation to crop domestication and improvement has been widely investigated. However, the contribution of epigenetic variation in crop domestication at population level has rarely been explored.




To understand the impact of epigenetics on crop domestication, we investigate the variation of DNA methylation during soybeandomestication and improvement by whole-genome bisulfite sequencing of 45 soybean accessions, including wild soybeans, landraces, and cultivars. Through methylomic analysis, we identify 5412 differentially methylated regions (DMRs). These DMRs exhibit characters distinct from those of genetically selected regions. In particular, they have significantly higher genetic diversity. Association analyses suggest only 22.54% of DMRs can be explained by local genetic variations. Intriguingly, genes in the DMRs that are not associated with any genetic variation are enriched in carbohydrate metabolism pathways.




This study provides a valuable map of DNA methylation across diverse accessions and dissects the relationship between DNA methylation variation and genetic variation during soybean domestication, thus expanding our understanding of soybean domestication and improvement.





Figure 1: Accession information and methylation sequencing. a Geographical distribution and phylogenetic tree of the 45 sequenced accessions. b Summary of whole-genome bisulfite sequencing. Statistics for reads pairs were the sum of all sequenced accessions, statistics for genome coverage and depth were the average of all sequenced accessions