Abstract
BackgroundDNA methylation is an important epigenetic modification. It can regulate the expression of many key genes without changing the primary structure of the genomic DNA, and plays a vital role in the growth and development of the organism. The genome-wide DNA methylation profile of the cytoplasmic male sterile (CMS) line in soybean has not been reported so far.ResultsIn this study, genome-wide comparative analysis of DNA methylation between soybean CMS line NJCMS5A and its maintainer NJCMS5B was conducted by whole-genome bisulfite sequencing. The results showed 3527 differentially methylated regions (DMRs) and 485 differentially methylated genes (DMGs), including 353 high-credible methylated genes, 56 methylated genes coding unknown protein and 76 novel methylated genes with no known function were identified. Among them, 25 DMRs were further validated that the genome-wide DNA methylation data were reliable through bisulfite treatment, and 9 DMRs were confirmed the relationship between DNA methylation and gene expression by qRT-PCR. Finally, 8 key DMGs possibly associated with soybean CMS were identified.ConclusionsGenome-wide DNA methylation profile of the soybean CMS line NJCMS5A and its maintainer NJCMS5B was obtained for the first time. Several specific DMGs which participated in pollen and flower development were further identified to be probably associated with soybean CMS. This study will contribute to further understanding of the molecular mechanism behind soybean CMS.
Highlights
DNA methylation is an important epigenetic modification
383,901,574 (NJCMS5A) and 398,207,546 (NJCMS5B) raw reads were generated from the two DNA library samples by whole-genome bisulfite sequencing (Table 1)
47.37%, 37.27% and 6.73% of cytosines were methylated in CG, CHG and CHH contexts of NJCMS5B, respectively (Fig. 1a)
Summary
DNA methylation is an important epigenetic modification. It can regulate the expression of many key genes without changing the primary structure of the genomic DNA, and plays a vital role in the growth and development of the organism. The genome-wide DNA methylation profile of the cytoplasmic male sterile (CMS) line in soybean has not been reported so far. DNA methylation level varies from 4.6% to 30% in plant, which is relatively higher than that in animal [13]. DNA methylation is supposed to impact the transcriptional level of genes by silencing TE; whereas, within the gene body, DNA methylation may be associated with highly-expressed genes [15]. Genes that encode DNMT have been isolated from a variety of plants, including rice, tobacco, corn and soybean [16,17,18,19,20]
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