Insights into epigenetics suggest a role of DNA methylation in regulating Chinese yam tuber shape

Plant organ shape is an important trait in terms of economic efficiency in agriculture. The club-like or spindle-shaped underground tubers of Chinese yam (Dioscorea polystachya Turcz.) impede mechanical harvest resulting in unprofitable cultivation. We performed genome-wide DNA methylation sequencing of two closely related Chinese yam tuber shape variants F60 (long, thin) and F2000 (short, thick) to investigate potential epigenetic effects on tuber development and shaping. Analysis of differentially methylated regions (DMRs) led to the identification of 1,513 hyper- or hypomethylated regions in 763 DMR-associated genes of which the majority were detected in the CHG methylation context. Gene Ontology (GO) term analysis revealed enriched DMR-associated genes related to anatomical structure development, hormone response, and photomorphogenesis. DMRs in brassinosteroid (BR) pathway-related genes, in particular BR signaling genes, were detected. We further identified hyperDMRs and hypoDMRs in putative circadian rhythm-related genes such as DpVOZ1, DpPIE1 and DpSPA1 as well as several putative organ shape-related genes (DpIQD13, DpTCPs). A potential network consisting of components of the BR signaling pathway, and circadian clock as well as microtubule-associated proteins was suggested to coordinate tuberization and affect tuber shape of Chinese yam.