Changes in genomic methylation patterns during the formation of triploid asexual dandelion lineages

Abstract

DNA methylation is an epigenetic mechanism that has the potential to affect plant phenotypes and that is responsive to environmental and genomic stresses such as hybridization and polyploidization. We explored de novo methylation variation that arises during the formation of triploid asexual dandelions from diploid sexual mother plants using methylation-sensitive amplified fragment length polymorphism (MS-AFLP) analysis. In dandelions, triploid apomictic asexuals are produced from diploid sexual mothers that are fertilized by polyploid pollen donors. We asked whether the ploidy level change that accompanies the formation of new asexual lineages triggers methylation changes that contribute to heritable epigenetic variation within novel asexual lineages. Comparison of MS-AFLP and AFLP fragment inheritance in a diploid x triploid cross revealed de novo methylation variation between triploid F(1) individuals. Genetically identical offspring of asexual F(1) plants showed modest levels of methylation variation, comparable to background levels as observed among sibs in a long-established asexual lineage. Thus, the cross between ploidy levels triggered de novo methylation variation between asexual lineages, whereas it did not seem to contribute directly to variation within new asexual lineages. The observed background level of methylation variation suggests that considerable autonomous methylation variation could build up within asexual lineages under natural conditions.

Genetic and epigenetic variation in Spartina alterniflora following the Deepwater Horizon oil spill

“…However, DNA methylation has been posited as a mechanism of phenotypic plasticity as well as a marker of stress response, and a number of studies have found a relationship between epigenetic variation and environment in support of this hypothesis (Herman & Sultan, 2016; Jablonka & Raz, 2009; Verhoeven, Jansen, et al., 2010; Verhoeven, Van Dijk, et al. 2010). Environmental stressors can induce variation in DNA methylation and in some cases, these environmentally induced methylation patterns can be inherited (Herrera & Bazaga, 2010, 2011; Verhoeven, Jansen, et al., 2010; Verhoeven, Van Dijk, et al.…”

“…Environmental stressors can induce variation in DNA methylation and in some cases, these environmentally induced methylation patterns can be inherited (Herrera & Bazaga, 2010, 2011; Verhoeven, Jansen, et al., 2010; Verhoeven, Van Dijk, et al. 2010), suggesting the potential for a signature of environmental response that is partially distinct from genetic variation.…”

“…This association between DNA methylation and plant ecology may reflect the modulation of gene expression (Bewick et al., 2016; Zilberman, Gehring, Tran, Ballinger, & Henikoff, 2007) or recombination rates (Mirouze et al., 2012), the release of transposable elements (Dowen et al., 2012), or other regulatory processes in response to environmental conditions in addition to covariance with genetic structure. In some cases, epigenetic variation can be restructured during periods of environmental stress and these changes can persist after the stress is relieved (Verhoeven, Jansen, van Dijk, Biere, 2010; Verhoeven, Van Dijk, Biere, 2010; Dowen et al., 2012 but see Wibowo et al., 2016). These findings suggest that epigenetic mechanisms may allow for rapid modification of phenotype in response to immediate and acute stressors (Rapp & Wendel, 2005).…”

“…Further, we anticipated a concurrent but stronger epigenetic signature of oil exposure, given its reflection of gene expression and physiological response to environmental stimuli (Dowen et al., 2012; Verhoeven, Jansen, et al., 2010; Verhoeven, Van Dijk, et al. 2010; Xie et al., 2015). …”

Genetic and epigenetic variation in a cosmopolitan grass Poa annua from Antarctic and Polish populations

“…Thus, such regions may regulate gene activ− ity or transcriptional silencing (Finnegan 2001(Finnegan , 2010. DNA methylation can be in− herited influencing various plant traits (Henderson and Jacobsen 2007;Jablonka 2009;Verhoeven et al 2010). It may also provide some features allowing to survive in novel environments (Lira−Medeiros et al 2010).…”