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Abstract
DNA methylation on cytosine residues is known to affect gene expression and is potentially responsible for the phenotypic variations among different crop cultivars. Here, we present the whole-genome DNA methylation profiles and assess the potential effects of single nucleotide polymorphisms (SNPs) for two mungbean cultivars, Sunhwanogdu (VC1973A) and Kyunggijaerae#5 (V2984). By measuring the DNA methylation levels in leaf tissue with the bisulfite sequencing (BSseq) approach, we show both the frequencies of the various types of DNA methylation and the distribution of weighted gene methylation levels. SNPs that cause nucleotide changes from/to CHH – where C is cytosine and H is any other nucleotide – were found to affect DNA methylation status in VC1973A and V2984. In order to better understand the correlation between gene expression and DNA methylation levels, we surveyed gene expression in leaf tissues of VC1973A and V2984 using RNAseq. Transcript expressions of paralogous genes were controlled by DNA methylation within the VC1973A genome. Moreover, genes that were differentially expressed between the two cultivars showed distinct DNA methylation patterns. Our mungbean genome-wide methylation profiles will be valuable resources for understanding the phenotypic variations between different cultivars, as well as for molecular breeding.
Highlights
We applied the BSseq method to genomic DNA extracted from the leaf tissues of two mungbean genotypes, VC1973A and V2984
To generate a DNA methylation map at the single base resolution across the mungbean genome, whole-genome bisulfite sequencing (BSseq or MethylC-seq)[3] was performed on genomic DNA isolated from Sunhwanogdu (VC1973A) and Kyunggijaerae#5 (V2984) leaves in the V1 growth stage
We found that in the mungbean genome, the overall proportion of mCHH DNA methylation was the highest compared to the other possible methylation sites examined
Summary
We applied the BSseq method to genomic DNA extracted from the leaf tissues of two mungbean genotypes, VC1973A and V2984. The gene expression levels in leaf tissues were measured by RNAseq Using this strategy, we were able to successfully profile the DNA methylation status of the mungbean genome and compared the methylation patterns of the VC1973A and V2984 cultivars to identify possible obligate epialleles that may serve as important genetic markers for breeding. We found cases where genes that were differentially expressed in the two cultivars contained distinct DNA methylation patterns. These results will be valuable for unraveling the role of DNA methylation in plant gene expression and will serve as an important genomic resource for understanding the phenotypic variations of mungbean cultivars for breeding
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