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Title: Dynamic changes of genome-wide DNA methylation during soybean seed development

item An, Yong-Qiang - Charles
item Goettel, Herbert
item HAN, QIANG - St Louis University
item BARTELS, ARTHUR - St Louis University
item Liu, Zongrang
item XIAO, WENYAN - St Louis University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/10/2017
Publication Date: 9/25/2017
Publication URL:
Citation: An, Y., Goettel, H.W., Han, Q., Bartels, A., Liu, Z., Xiao, W. 2017. Dynamic changes of genome-wide DNA methylation during soybean seed development. Scientific Reports. 7:12263.

Interpretive Summary: Seed maturation is one of the most important biological processes in soybean agriculture that directly affects seed quality and seed yield, two of the most important soybean agronomic traits. Natural and specific methylation of DNA, a chemical modification by the addition of a methyl group, in the nucleus has been demonstrated to play a critical regulatory role in a variety of plant biological processes. However, its role in the genetic control of soybean seed maturation is less understood. We applied a highly effective large-scale technology called whole-genome bisulfite sequencing (mapping of methyl groups on the DNA molecule for the whole genome) to demonstrate that DNA methylation of soybean seed is highly dynamic during maturation. We were able to identify a collection of DNA sequence blocks that were differentially methylated during maturation. The seed-maturation associated genes and pathways that are potentially regulated by DNA methylation were also identified. This study will lay a foundation for further investigation of DNA modification in regulating the genetic programs that drive seed maturation and thus offers a new strategy and approach for the genetic manipulation to improve soybean seed quality and yields.

Technical Abstract: Seed development is programmed by expression of many genes in plants. Seed maturation is an important developmental process to soybean seed quality and yield. DNA methylation is a major epigenetic modification regulating gene expression. However, little is known about the dynamic nature of DNA methylation and its effects on gene expression during plant development. Through whole-genome bisulfite sequencing, we showed that DNA methylation went through dynamic changes during seed maturation. An average of 66% CG, 45% CHG and 9% CHH contexts was methylated in cotyledons. CHH methylation levels in cotyledons changed greatly from 6% at the early stage to 11% at the late stage. Transcribed genes were approximately two-fold more likely to be differentially methylated than non-transcribed genes. We identified 40, 66 and 2136 genes containing differentially methylated regions (DMRs) with negative correlation between their methylation and expression in the CG, CHG and CHH contexts, respectively. The majority of the DMR genes in the CHH context were transcriptionally down-regulated as seeds mature: 99% of them during early seed maturation have a preferential association with DNA replication and cell division. The results provide novel insights into the dynamic nature of DNA methylation and its relationship with gene regulation in seed development.