Quantitative trait variation is revealed in a novel hypomethylated population of woodland strawberry (Fragaria vesca)

Abstract

BackgroundPhenotypic variation is determined by a combination of genotype, environment and their interactions. The realization that allelic diversity can be both genetic and epigenetic allows the environmental component to be further separated. Partitioning phenotypic variation observed among inbred lines with an altered epigenome can allow the epigenetic component controlling quantitative traits to be estimated. To assess the contribution of epialleles on phenotypic variation and determine the fidelity with which epialleles are inherited, we have developed a novel hypomethylated population of strawberry (2n = 2x = 14) using 5-azacytidine from which individuals with altered phenotypes can be identified, selected and characterized.ResultsThe hypomethylated population was generated using an inbred strawberry population in the F. vesca ssp. vesca accession Hawaii 4. Analysis of whole genome sequence data from control and hypomethylated lines indicate that 5-azacytidine exposure does not increase SNP above background levels. The populations contained only Hawaii 4 alleles, removing introgression of alternate F. vesca alleles as a potential source of variation. Although genome sequencing and genetic marker data are unable to rule out 5-azacytidine induced chromosomal rearrangements as a potential source of the trait variation observed, none were detected in our survey. Quantitative trait variation focusing on flowering time and rosette diameter was scored in control and treated populations where expanded levels of variation were observed among the hypomethylated lines. Methylation sensitive molecular markers indicated that 5-azacytidine induced alterations in DNA methylation patterns and inheritance of methylation patterns were confirmed by bisulfite sequencing of targeted regions. It is possible that methylation polymorphisms might underlie or have induced genetic changes underlying the observable differences in quantitative phenotypes.ConclusionsThis population developed in a uniform genetic background provides a resource for the discovery of new variation controlling quantitative traits. Genome sequence analysis indicates that 5-azacytidine did not induce point mutations and the induced variation is largely restricted to DNA methylation. Using this resource, we have identified new variation and demonstrated the inheritance of both variant trait and methylation patterns. Although direct associations remain to be determined, these data suggest epigenetic variation might be subject to selection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0936-8) contains supplementary material, which is available to authorized users.

Stable Epigenetic Variants Selected from an Induced Hypomethylated Fragaria vesca Population

“…We used the DNA demethylation reagent 5-azacytidine (5-azaC) as a tool to induce and broaden phenotypic diversity in Fragaria vesca . In a previous study, we showed 5-azaC does not induce mutations to the primary DNA sequence (Xu et al, 2016). …”

“…F. vesca is a useful model system to examine the transmission of phenotypic traits induced by epigenetic variation due to its short 3.5 month seed to seed life cycle in the greenhouse and modified stems (stolons) to clonally propagate daughter plants. Here, we used the diploid F. vesca lines identified from the hypomethylated population generated in a previous study (Xu et al, 2016) to investigate the inheritance of variant traits including early and late flowering time, and late stolon emergence time. The question of whether the lines with specific phenotypic traits possess varied epigenetic status and can be subject to selection was explored in this study.…”

Tissue-Specific Response to Experimental Demethylation at Seed Germination in the Non-Model Herb Erodium cicutarium

“…In flax, a short duration treatment with a high 5azaC concentration (1.5 mM) generated more stable early flowering epimutants [16,41,54]. In strawberry [42], an increased phenotypic variance was obtained at intermediate concentrations (20-50 mM), whereas the highest one (100 mM) was entirely detrimental. Altogether, current evidence suggests that 5azaC may have a slightly larger and more stable effect in DNA although the most practical concentration to induce phenotypic variance without reducing survival can vary among species.…”

“…The phenotypic consequences of the cell reprogramming associated to genome-wide demethylation, however, are not necessarily the same across species, genetic backgrounds, and cell lines [13]. For instance, the application of 5azaC induced metastable early flowering lines in flax [41], delayed flowering in some but not all of A. thaliana genetic lines assayed [21] and both early and late flowering lines in strawberry [42]. In this study, we documented a reduction in leaf size and leaf production during early seedling development in E. cicutarium that was treated with 5azaC.…”

“…In particular, experimental demethylation with DNMTi has contributed to reveal the broad range of plant traits and developmental processes that are regulated through DNA cytosine methylation, because such experiments have been able to, among others, alter sex expression [15], modify growth, leaf traits, flowering time or fruit ripening (e.g., [17,18,21,[41][42][43][44]), and induce dwarfism at maturity [14,17]. The phenotypic consequences of the cell reprogramming associated to genome-wide demethylation, however, are not necessarily the same across species, genetic backgrounds, and cell lines [13].…”