Autopolyploidization in switchgrass alters phenotype and flowering time via epigenetic and transcription regulation

Abstract

Polyploidization is a significant source of genomic and organism diversification during plant evolution, and leads to substantial alterations in plant phenotypes and natural fitness. To help understand the phenotypic and molecular impacts of autopolyploidization, we conducted epigenetic and full-transcriptomic analyses of a synthesized autopolyploid accession of switchgrass (Panicum virgatum) in order to interpret the molecular and phenotypic changes. We found that mCHH levels were decreased in both genic and transposable element (TE) regions, and that TE methylation near genes was 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. In addition, up-regulated PvTOE1 and suppressed PvFT probably contribute to later flowering time of the autopolyploid. The expression changes were probably associated with modification of nearby methylation sites and siRNAs. We also experimentally demonstrated that expression levels of PvFT and PvTOE1 were regulated by DNA methylation, supporting the link between alterations in methylation induced by polyploidization and the phenotypic changes that were observed. Collectively, our results show epigenetic modifications in synthetic autopolyploid switchgrass for the first time, and support the hypothesis that polyploidization-induced methylation is an important cause of phenotypic alterations and is potentially important for plant evolution and improved fitness.

Comparative transcriptome study of switchgrass (Panicum virgatum L.) homologous autopolyploid and its parental amphidiploid responding to consistent drought stress

“…In this study, we use 8X Alamo and 4X Alamo to process the drought treatment at various time points, followed by physiological and transcriptional analyses. Our previous study found that the sequence of 8X and 4X Alamo switchgrass were 99% identical with each other [52]. The analyses of this study could provide insights about drought the mechanism of response in switchgrass at both physiological and transcriptional levels before/after WGD and also provide abundant data for the drought tolerant breeding of switchgrass.…”

Altered chromatin conformation and transcriptional regulation in watermelon following genome doubling

“…Considering that phenotype changes due to polyploidy in isogenic individuals cannot be related to sequence-based regulatory differences, DNA methylation level differences might be implicated. Studies identifying differentially methylated regions (DMRs) in diploids and autopolyploids of Arabidopsis, rice and switchgrass support this idea (Yan et al, 2019;Yu et al, 2010;Zhang et al, 2015).…”

Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure

“…Newly created autopolyploids can contain epigenetic modifications, e.g. switchgrass [53] and Arabidopsis [54], but effects on gene expression are much smaller than in allopolyploids [55] and occur rather stochastically [56].…”