DNA methylome and transcriptome associate analysis of somaclone variation tissue in pineapple

Somaclones in tissue culture is a common phenomena appearing due to external or internal environmental conditions. These changes in phenotype may result due to heritable changes in gene expression or can be non-heritable. One mechanism involves with these changes are are epigenetic modifications and these changes affect plant growth and development. The highly dynamic epigenome alter with environmental changes response through changing gene expression pattern. DNA methylation is one of epigenetics changes resulted mutations in tissue cultured pineapple plants. In this study, we have observed changes in the chlorophyll development with changes in methylation pattern. We performed DNA methylome and transcriptome analysis of mutants and normal green plants (WT). The DNA methylation patterns and levels of these tissues showed reduction in methylation level in all three contexts in mutants compared to WT. Further, we noticed reduction in the methyation level in the gene body region compared to the upstream and downstream regions in th CHG and CHH contexts. We identified thousands of differentially methyated regions (DMRs) in the mutants and thousands of genes overlapped with DMRs. They were differentially expressed and some of those genes involved with chlorophyll metabolism. With the result of analysis, we can conclede that changes in methylation resulted mutants with changes in chlorophyll metabolism resulting different in leaf colour.