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 th… Show more
“…Cytosine residues methylated in the CpG context showed the largest difference in methylation levels in genic DMRs, whereas those methylated in the CHH context showed the lowest difference in methylation levels (Table S4 ). This result was consistent with the previous observation that methylation level of CHH had the least effect on gene expression levels in mungbean 11 . Figure 2 Average methylation levels of cytosines on genic DMRs ( A ) where methylation level is significantly higher in high SPM group than low SPM group (hhDMRs) and ( B ) where methylation level is significantly higher in low SPM group than high SPM group (hlDMRs).…”
Section: Resultssupporting
confidence: 93%
“…Cytosine residues methylated in the CpG context showed the largest difference in methylation levels in genic DMRs, whereas those methylated in the CHH context showed the lowest difference in methylation levels (Table S4). This result was consistent with the previous observation that methylation level of CHH had the least effect on gene expression levels in mungbean 11 .…”
Section: Methylation Levels At Genic Dmrs the Distribution Of Methylsupporting
confidence: 93%
“…Fig. 3) 11 . The difference in methylation status possibly affected the difference in expression levels of these genes between VC1973A and V2984, independent of nucleotide sequence variation.…”
Section: Methylation Levels At Genic Dmrs the Distribution Of Methylmentioning
confidence: 99%
“…In tomato (Solanum lycopersicum L.) fruits, vitamin E content is determined by epialleles 10 . Although genome-wide DNA methylation patterns have been investigated in two mungbean genotypes, VC1973A and V2984, epigenetic factors associated with any agronomic trait have not been studied in mungbean 5,11 .…”
Cytosine methylation in genomic DNA affects gene expression, potentially causing phenotypic variation. Mungbean, an agronomically and nutritionally important legume species, is characterized by nonsynchronous pod maturity, resulting in multiple harvest which costs extra time and labor. To elucidate the epigenetic influences on synchronous pod maturity (SPM) in mungbean, we determined the genome-wide DNA methylation profiles of eight mungbean recombinant inbred lines (RILs) and their parental genotypes, and compared DNA methylation profiles between high SPM and low SPM RILs, thus revealing differentially methylated regions (DMRs). A total of 3, 18, and 28 pure DMRs, defined as regions showing no significant correlation between nucleotide sequence variation and methylation level, were identified in CpG, CHG, and CHH contexts, respectively. These DMRs were proximal to 20 genes. Among the 544 single nucleotide polymorphisms identified near the 20 genes, only one caused critical change in gene expression by early termination. Analysis of these genome-wide DNA methylation profiles suggests that epigenetic changes can influence the expression of proximal genes, regardless of nucleotide sequence variation, and that SPM is mediated through gibberellin-mediated hormone signaling pathways. These results provide insights into how epialleles contribute to phenotypic variation and improve SPM in mungbean cultivars.
“…Cytosine residues methylated in the CpG context showed the largest difference in methylation levels in genic DMRs, whereas those methylated in the CHH context showed the lowest difference in methylation levels (Table S4 ). This result was consistent with the previous observation that methylation level of CHH had the least effect on gene expression levels in mungbean 11 . Figure 2 Average methylation levels of cytosines on genic DMRs ( A ) where methylation level is significantly higher in high SPM group than low SPM group (hhDMRs) and ( B ) where methylation level is significantly higher in low SPM group than high SPM group (hlDMRs).…”
Section: Resultssupporting
confidence: 93%
“…Cytosine residues methylated in the CpG context showed the largest difference in methylation levels in genic DMRs, whereas those methylated in the CHH context showed the lowest difference in methylation levels (Table S4). This result was consistent with the previous observation that methylation level of CHH had the least effect on gene expression levels in mungbean 11 .…”
Section: Methylation Levels At Genic Dmrs the Distribution Of Methylsupporting
confidence: 93%
“…Fig. 3) 11 . The difference in methylation status possibly affected the difference in expression levels of these genes between VC1973A and V2984, independent of nucleotide sequence variation.…”
Section: Methylation Levels At Genic Dmrs the Distribution Of Methylmentioning
confidence: 99%
“…In tomato (Solanum lycopersicum L.) fruits, vitamin E content is determined by epialleles 10 . Although genome-wide DNA methylation patterns have been investigated in two mungbean genotypes, VC1973A and V2984, epigenetic factors associated with any agronomic trait have not been studied in mungbean 5,11 .…”
Cytosine methylation in genomic DNA affects gene expression, potentially causing phenotypic variation. Mungbean, an agronomically and nutritionally important legume species, is characterized by nonsynchronous pod maturity, resulting in multiple harvest which costs extra time and labor. To elucidate the epigenetic influences on synchronous pod maturity (SPM) in mungbean, we determined the genome-wide DNA methylation profiles of eight mungbean recombinant inbred lines (RILs) and their parental genotypes, and compared DNA methylation profiles between high SPM and low SPM RILs, thus revealing differentially methylated regions (DMRs). A total of 3, 18, and 28 pure DMRs, defined as regions showing no significant correlation between nucleotide sequence variation and methylation level, were identified in CpG, CHG, and CHH contexts, respectively. These DMRs were proximal to 20 genes. Among the 544 single nucleotide polymorphisms identified near the 20 genes, only one caused critical change in gene expression by early termination. Analysis of these genome-wide DNA methylation profiles suggests that epigenetic changes can influence the expression of proximal genes, regardless of nucleotide sequence variation, and that SPM is mediated through gibberellin-mediated hormone signaling pathways. These results provide insights into how epialleles contribute to phenotypic variation and improve SPM in mungbean cultivars.
“… 19 revealed a correlation between whole genome methylation and polyploidy in soybean and common bean. Further, specific DNA methylation patterns have been speculated to be potentially responsible for phenotypic variations between different cultivars of common bean and mung bean 20 . However, despite the well-established roles of DNA methylation in several plant species, DNA methylation in chickpea has not been investigated till date.…”
DNA methylation is widely known to regulate gene expression in eukaryotes. Here, we unraveled DNA methylation patterns in cultivated chickpea to understand the regulation of gene expression in different organs. We analyzed the methylation pattern in leaf tissue of wild chickpea too, and compared it with cultivated chickpea. Our analysis indicated abundant CG methylation within gene-body and CHH methylation in intergenic regions of the chickpea genome in all the organs examined. Analysis of differentially methylated regions (DMRs) demonstrated a higher number of CG context DMRs in wild chickpea and CHH context DMRs in cultivated chickpea. We observed increased preponderance of hypermethylated DMRs in the promoter regions and hypomethylated DMRs in the genic regions in cultivated chickpea. Genomic location and context of the DMRs correlated well with expression of proximal genes. Our results put forth a positive correlation of promoter hypermethylation with increased transcript abundance via identification of DMR-associated genes involved in flower development in cultivated chickpea. The atypical correlation observed between promoter hypermethylation and increased transcript abundance might be dependent on 24-nt small RNAs and transcription factors binding to the promoter region. This study provides novel insights into DNA methylation patterns in chickpea and their role in regulation of gene expression.
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