WGD shifts phenotypic and flowering time via epigenetic and transcription regulations in switchgrass

Polyploidization is a significant source of genomic and organism diversification during plant evolution, leading to substantial alterations on plant phenotypes and natural fitness. To understand the phenotypic and molecular impacts of autopolyploidization, we conducted epigenetic and full-transcriptomic analyses, to interpret the molecular and phenotypic changes, of a synthesized autopolyploid switchgrass. Results showed mCHH levels were decreased in both genic and transposable element (TE) regions and TE methylation near genes were decreased as well. Among 142 differentially expressed genes involved in cell division, cellulose biosynthesis, auxin response, growth, and reproduction processes, 75 of them were modified by 122 differentially methylated regions, 10 miRNAs, and 15 siRNAs. Also, Up-regulated PvTOE1 and suppressed PvFT likely contribute to later flowering time of the autopolyploid. The expression changes were likely associated with modification of nearby methylation sites and siRNAs. We also experimentally proved that expression levels of PvFT and PvTOE1 were regulated by DNA methylation treatment, supporting the link of polyploidization-induced methylation alteration with their phenotypic change. Collectively, these results, for the first time, showed epigenetic modifications on the synthetic autopolyploid switchgrass, and supported the hypothesis of polyploidization-induced methylation was an important cause for phenotypic alteration and potentially for plant evolution for better natural fitness.