title: Genome-wide DNA methylation profile in mungbean.
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.
authors.affiliation: Department of Plant Science and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
authors.forename: Yang Jae
authors.initials: YJ
authors.lastname: Kang
authors.affiliation: Department of Plant Science and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
authors.forename: Ahra
authors.initials: A
authors.lastname: Bae
authors.affiliation: Department of Plant Science and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
authors.forename: Sangrea
authors.initials: S
authors.lastname: Shim
authors.affiliation: Department of Plant Science and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
authors.forename: Taeyoung
authors.initials: T
authors.lastname: Lee
authors.affiliation: Department of Plant Science and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
authors.forename: Jayern
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Plant Science and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.|Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor 16111, Indonesia.
authors.forename: Dani
authors.initials: D
authors.lastname: Satyawan
authors.affiliation: Department of Plant Science and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.|Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Korea.
authors.forename: Moon Young
authors.initials: MY
authors.lastname: Kim
authors.affiliation: Department of Plant Science and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.|Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-921, Korea.
authors.forename: Suk-Ha
authors.initials: SH
authors.lastname: Lee
mesh_terms: D001483:Base Sequence; D019175:DNA Methylation / Q000235:genetics*; D020440:Gene Duplication; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics; D000070658:Vigna / Q000235:genetics*