Decoding the sorghum methylome: understanding epigenetic contributions to agronomic traits

Abstract

DNA methylation is a chromatin modification that plays an essential role in regulatinggene expression and genome stability and it is typically associated with gene silencingand heterochromatin. Owing to its heritability, alterations in the patterns of DNA methyla-tion have the potential to provide for epigenetic inheritance of traits. Contemporary epige-nomic technologies provide information beyond sequence variation and could supplyalternative sources of trait variation for improvement in crops such as sorghum. Yet, com-pared with other species such as maize and rice, the sorghum DNA methylome is farless well understood. The distribution of CG, CHG, and CHH methylation in the genomeis different compared with other species. CG and CHG methylation levels peak aroundcentromeric segments in the sorghum genome and are far more depleted in the genedense chromosome arms. The genes regulating DNA methylation in sorghum are also yetto be functionally characterised; better understanding of their identity and functional ana-lysis of DNA methylation machinery mutants in diverse genotypes will be important tobetter characterise the sorghum methylome. Here, we catalogue homologous genesencoding methylation regulatory enzymes in sorghum based on genes inArabidopsis,maize, and rice. Discovering variation in the methylome may uncover epialleles thatprovide extra information to explain trait variation and has the potential to be applied inepigenome-wide association studies or genomic prediction. DNA methylation can alsoimprove genome annotations and discover regulatory elements underlying traits. Thus,improving our knowledge of the sorghum methylome can enhance our understanding ofthe molecular basis of traits and may be useful to improve sorghum performance.