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Predictable and stable epimutations induced during clonal plant propagation with embryonic transcription factor [1]

['Anjar Tri Wibowo', 'School Of Life Science', 'University Of Warwick', 'Coventry', 'United Kingdom', 'Department Of Molecular Biology', 'Max Planck Institute For Developmental Biology', 'Tubingen', 'Department Of Biology', 'Faculty Of Science']

Date: 2022-12 

Clonal propagation is frequently used in commercial plant breeding and biotechnology programs because it minimizes genetic variation, yet it is not uncommon to observe clonal plants with stable phenotypic changes, a phenomenon known as somaclonal variation. Several studies have linked epigenetic modifications induced during regeneration with this newly acquired phenotypic variation. However, the factors that determine the extent of somaclonal variation and the molecular changes underpinning this process remain poorly understood. To address this gap in our knowledge, we compared clonally propagated Arabidopsis thaliana plants derived from somatic embryogenesis using two different embryonic transcription factors- RWP-RK DOMAIN-CONTAINING 4 (RKD4) or LEAFY COTYLEDON2 (LEC2) and from two epigenetically distinct founder tissues. We found that both the epi(genetic) status of the explant and the regeneration protocol employed play critical roles in shaping the molecular and phenotypic landscape of clonal plants. Phenotypic variation in regenerated plants can be largely explained by the inheritance of tissue-specific DNA methylation imprints, which are associated with specific transcriptional and metabolic changes in sexual progeny of clonal plants. For instance, regenerants were particularly affected by the inheritance of root-specific epigenetic imprints, which were associated with an increased accumulation of salicylic acid in leaves and accelerated plant senescence. Collectively, our data reveal specific pathways underpinning the phenotypic and molecular variation that arise and accumulate in clonal plant populations.

Clonal propagation is commonly used in plants to propagate selected genotypes and to aid genetic/genomic manipulation. Although cloning minimizes genetic variation, clonal plants commonly display phenotypic changes, a phenomenon known as somaclonal variation, that are at times stable after multiple cycles of sexual reproduction. The newly acquired phenotypic variation exhibited by clonal plants has been linked to non-genetic modifications induced during the regeneration process, though the precise nature of these modifications and the factors implicated remain poorly understood. By generating clonal plants through two different methods and using two distinct tissues–roots and leaves–, we show that the phenotypic variation found in clonal plants is linked to heritable changes in DNA methylation marks already present in the founder tissues. Further, these novel phenotypes are associated with specific patterns of gene expression and metabolic changes. Our findings unveil specific pathways underpinning new phenotypic and molecular variation that arises and accumulates in clonal plant populations.

Funding: This work was supported by ERA-CAPS AUREATE (DFG) and the Max Planck Society to (DW), an European Research Council (ERC) Marie Skłodowska-Curie Fellowship (751204-H2020-MSCA-IF-2016) and Airlangga University Hibah Riset Mandat Grant (387/UN3.14/PT/2020) to (ATW), and BBSRC grants (BB/L003023/1, BB/N005279/1, BB/N00194X/1 and BB/P02601X/1) to (JGM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

A key characteristic of asexual propagation is that the individuals produced are genetically identical to their parents, except for a few spontaneous de novo mutations [ 1 ]. However, clonal plants often display heritable phenotypic variation [ 11 , 12 ], known as somaclonal variation, which is linked to genetic [ 13 , 14 ] and epigenetic changes [ 12 , 15 , 16 ]. Moreover, this phenotypic diversity could contribute to the adaptation to recurrent environmental challenges. In a previous study we found that Arabidopsis plants regenerated through the ectopic activation of an embryonic transcription factor, resulted in clonal plants that inherited molecular signatures, DNA methylation and gene expression profiles, characteristic of the tissue of origin [ 12 ]. Whether this molecular and phenotypic variation is primarily caused by the direct regeneration of clonal individuals from different above and belowground organs, or driven by the organ-specific activity of the embryonic transcription factor employed, has been unclear. To address this gap in our knowledge, we generated clonal progeny from Arabidopsis roots and leaves through the ectopic activation of two different embryonic transcription factors. We found that the founder organ employed for cloning significantly contributes to clonal progeny, with root regenerants inheriting tissue-specific DNA methylation imprints and transcriptional states, independent of the regeneration method used. Results from our study reveals avenues for the manipulation of phenotypic traits through cloning for the adoption in crop improvement programs.

Many multicellular organisms can reproduce both sexually and asexually, with clonal reproduction being especially common in plants, where it is prevalent in ferns, mosses and many angiosperms [ 1 , 2 ]. Most plant species can switch to asexual reproductive programs in response to environmental stimuli by forming specialized structures such as rhizomes, stolons and bulbils [ 2 ]. Such flexibility in reproductive strategies is thought to be possible due to the high degree of plasticity and totipotency of plant cells. This property has been traditionally exploited for the clonal propagation and genomic manipulation of many economically important species [ 3 ]. Clonal propagation can be achieved in different ways, from simple methods such as grafting and cuttings to more advanced methods such as tissue culture-induced regeneration using phytohormones or embryonic/meristematic transcription factors. In Arabidopsis thaliana (hereafter, Arabidopsis), somatic embryogenesis (SE) and plant regeneration can be initiated through the ectopic overexpression of embryonic transcription factors such as AGAMOUS- LIKE15 (AGL15) [ 4 ], BABY BOOM (BBM) [ 5 ], LEAFY COTYLEDON2 (LEC2) [ 6 ], WUSCHEL (WUS) [ 7 – 9 ] and RWP-RK DOMAIN-CONTAINING 4 (RKD4) [ 10 ].

To understand how losses of DNA methylation at specific loci could cause the phenotype, we searched for deregulated genes in the proximity of the 36 DMRs. We found two genomic regions where methylation status co-segregated with the phenotype for both directions of the crosses ( Fig 4G ). One region included three genes in its proximity that are upregulated in leaves of RO-LEC2 regenerants ( Fig 4F ). The DMR is located in a TE of the AtSINE4 family, between two of the genes found to be misregulated in RO-LEC2 plants when compared to Ws-2/indLEC2 control ( Fig 4H ). We investigated the chromatin conformation of these regions in leaves and roots of wild-type plants, and found notable differences, thus suggesting it may act as a long-distance regulatory element for flanking genes ( S8 Fig ). Another DMR associated with early senescence in RO-LEC2 plants was located in an AtMUNX1 TE upstream of the PRE1/BNQ1 locus ( S9 Fig ), in a region flanking a CarG box known to be a target of MADS box containing transcription factors [ 18 ] and negatively regulated by the transcription factor pair APETALA3 (AP3) and PISTILLATA (PI) [ 19 ].

We investigated the mode of inheritance of RO imprints by generating DNA methylation profiles of leaves from F 2 progeny derived from Ws-2/indLEC2 x RO-LEC2 hybrids. If differences in DNA methylation were responsible for the growth phenotypes characteristic of RO plants, we reasoned the methylation imprints must be already present in the parents. We therefore focused on DMRs between leaves of Ws-2/indLEC2 and RO-LEC2 plants. Most regions that are hypomethylated in RO-LEC2 regenerants were stably inherited both mitotically and meiotically ( Fig 4B ). On the other hand, most hypermethylated DMRs had disappeared after two generations of paternal transmission, although they were faithfully inherited maternally ( Fig 4B ). This was observed for both CG- and CHG-hypermethylated DMRs, while CHH-hypermethylation was reset both paternally and maternally ( S7 Fig ). These data suggest that the early senescence phenotype observed in RO-LEC2 plants may be caused by an epimutation associated with a reduction in DNA methylation, as plants with early senescence appeared in both directions of the cross. After clustering samples based on the levels of methylation for DMRs, we found that CHH-hypomethylated DMRs as a class predicted phenotype, ( Fig 4C ), and this was clearest for RO-LEC2 x Ws-2/indLEC2 progeny. Thirty-six DMRs co-segregated with the growth phenotype. Normal plants were highly methylated, as in the Ws-2/indLEC2 control, and early senescing plants had low methylation at these 36 DMRs ( Fig 4D ). These phenotype-associated DMRs were strongly enriched in transposable elements (TEs) ( Fig 4E ). Collectively, these data suggest that demethylation of TEs is associated with early senescence of RO-LEC2 plants.

(A) Experimental design to identify epi- and DNA mutations linked to RO-LEC2 phenotypes. Green indicates phenotypically normal plants (n = 10) and brown early senescing ones (n = 10). Analysis was carried out using five independent F 2 progeny. (B) Heatmap showing gains and losses of CG methylation for RO-LEC2-leaf DMRs in F 2 progeny from reciprocal backcrosses between control (Ws-2/indLEC2) and RO-LEC2 plants. Each column represents an independent F 2 progeny individual. (C) Dendrogram of F 2 progeny and parents at parental CHH-hypo-DMRs. (D) Heatmap of Z-scores in CHH methylation for highly methylated (Ws-2/indLEC2%mC > 50) parental CHH-DMRs, showing clustering of parents and RO x Ws-2/indLEC2 F 2 progeny. (E) Annotation of several subsets of parental CHH DMRs to different genetic features compared to the distribution of features in the whole genome. Upstream and downstream are defined as 2 kb away from a gene and Intergenic as all sequences more than 2 kb away from any gene. The priority of annotations is Gene, TE, Upstream, Downstream and Intergenic in that order. (F) Expression levels from RNA-seq for genes proximal to Chr5:892411–894943 (AtSINE4) DMR in leaves of control (Ws-2/indLEC2) and regenerants. Asterisks represent significant differences, determined by Wald test and adjusted with the Bonferroni–Holm method: * p < 0.05, ** p < 0.01 (G) CHH methylation levels for Chr5:892411–894943 (AtSINE4) DMR in Ws-2/indLEC2, RO-LEC2, and F 2 reciprocal crosses, showing association between demethylation and morphological phenotype. (H) Genomic view around Chr5:892411–894943 (AtSINE4) DMR. Yellow box represents RO-LEC2 CHH-DMR.

To determine the molecular basis for the early senescence phenotype observed in RO regenerants, we performed reciprocal crosses between Ws-2 and RO-LEC2 plants. Five reciprocal F 1 hybrids were self-pollinated to generate F 2 seed progeny ( Fig 4A ). In the F 2 generation, some plants were early senescing, characteristic of RO-LEC2 plants, while others were not. The fraction of early-senescing plants was around one quarter, with 16% (13 in 80) early-senescing F 2 progeny derived from Ws-2/indLEC2 x RO-LEC2 hybrids, and 23% (28 in 120) early-senescing F 2 progeny derived from RO-LEC2 x Ws-2/indLEC2 hybrids (p>0.05, Fisher’s Exact test). These data suggest that early senescence in RO-LEC2 regenerants may be under the control of a single recessively acting locus. To determine whether this was due to a genetic mutation, we whole-genome shotgun sequenced 10 phenotypically normal and 10 early-senescing individuals from five different segregating F 2 populations ( Fig 4A ). However, we could not identify genetic variants linked to this phenotype ( S6 Fig ), suggesting that the phenotypes were caused by an epigenetic change.

When only considering DMRs distinguishing leaves and roots of non-regenerated plants, RO-LEC2 leaves, although distinct from other samples, resembled the methylation of root samples ( Fig 3B ). Most DMRs in leaves of RO-LEC2 regenerants were primarily hypomethylated compared to leaves of control plants, resembling the methylation profile of these regions in control roots, and they were stably inherited (Figs 3C and S4 ). Similar to roots of control plants, these DMRs were also hypomethylated in roots of LO-LEC2 regenerants, thus pointing to active DNA demethylation in Arabidopsis roots. Collectively, our analyses demonstrate that induction of somatic embryogenesis and subsequent regeneration results in tissue-specific epigenetic imprints that are stable during sexual reproduction.

(A) PCAs of CG DNA methylation levels at 226 CG-DMRs identified in all-against-all comparison and histograms of the distribution of samples across each principal component. Probability ellipses (95% distribution) for each group are shown. Gray, control; Blue, LO-LEC2; Red, RO-LEC2. Data from three randomly selected regenerants for each tissue. (B) PCA of CG methylation levels at 511 CG-DMRs identified in the comparison of control leaves and roots. Probability ellipses (95% distribution) for each group are shown. Gray, control; Blue, LO-LEC2; Red, RO-LEC2. Data from three randomly selected regenerants for each tissue. (C) Heatmap of CG methylation levels in leaves and roots of control plants and LEC2 regenerants. Each column corresponds to an independently regenerated line. Ws-2 = Ws-2/indLEC2. Data from three randomly selected regenerants for each tissue.

We postulated that the phenotypic and transcriptional changes found in plants regenerated with embryonic transcription factors may be caused by the inheritance of heritable tissue-specific epigenetic imprints. To test this hypothesis, we studied the methylome of LEC2 regenerants that had been propagated for two successive generations (G2 and G3). To map methylome data we generated a de novo assembly of the Ws-2 genome (see methods ). In an all-against-all comparison of RO-LEC2 and LO-LEC2 plants, we found 226, 120 and 386 Differentially Methylation Regions (DMRs) in CG, CHG and CHH contexts, respectively ( S3 Table ). Principal component analysis (PCA) of the 226 CG-DMRs showed that the main source of variance in our dataset was the tissue analyzed (69% of variance), with methylome profile of leaves of RO-LEC2 plants being slightly skewed towards root samples ( Fig 3A ). Another 6% of variance can be explained by the tissue of origin, separating RO-LEC2 and LO-LEC2 samples from each other and from the controls, independent of the tissue sampled. Some of the remaining variance (3%) comes from the regeneration process independent of tissue sampled or founder tissue used for cloning ( Fig 3A ). These data suggest that even though the methylome of regenerated plants mainly corresponds to the characteristic methylome of the tissue sampled, a number of epigenetic imprints are maintained from the tissue employed for cloning, even after plants had undergone three cycles of sexual reproduction. Our data also show that regeneration by itself contributes to discrete methylation imprints that are stably inherited in clonal plants ( S4 Fig ). Similar, albeit weaker patterns were observed for non-CG DMRs ( S4 Fig ). To define the potential impact of these epigenetic changes, we mapped DMRs to genome features, which revealed that regions flanking protein coding genes were particularly likely to be associated with methylation changes ( S5 Fig ).

To obtain further insight into the possible function of these DEGs, we performed Gene Ontology (GO) analyses, finding that DEGs in leaves from both RO-LEC2 and RO-RKD4 lines were enriched for stress and defense responses (FDR<0.05, Fig 2C ). In contrast, DEGs in roots from either LO-LEC2 or LO-RKD4 lines were primarily associated with metabolic processes ( Fig 2C ). Network analysis revealed that genes related to pathogen responses and senescence were upregulated in RO plants, independent of the embryonic transcription factor used for clonal propagation ( Fig 2D and 2E ). As several of the genes upregulated in RO-LEC2 leaves were part of the salicylic acid (SA) biosynthesis pathway ( Fig 2F ), we measured the concentration of total SA in G2 progenies of LEC2 regenerated plants. Reduced biomass and early senescence in RO-LEC2 lines were strongly associated with high levels of SA, indicating a causal relationship between transcriptional changes, differences in production of a defense hormone known to negatively affect growth and to induce early senescence [ 17 ], and morphological changes in the regenerants ( Fig 2G ). The senescence phenotypes observed are likely caused by the disturbance of free SA and conjugated SA. Collectively, our analyses revealed that the clonal propagation of plants using embryonic transcription factors results in the transmission of organ-specific transcriptional states.

(A) Number of DEGs for different comparisons split by FDR levels. Data from three randomly selected regenerants for each tissue. (B) Euler diagram of common DEGs found in RO plants regenerated using two different transcription factors. p-value indicates results from Fisher’s exact test. (C) Gene Ontology analysis showing significant enrichment for stress-related genes among DEGs in RO-LEC2 (left) and RO-RKD4 (right) leaves. Categories are sorted by decreasing FDR. (D) Interaction network of DEGs found in leaves of RO-LEC2 plants. Orange, upregulated genes; blue, downregulated genes; green, non-DEGs with significant interactions with the network. Diamond shaped nodes, transcription factors. Main GO terms associated with clusters are highlighted. (E) Interaction network of DEGs found in leaves of RO-RKD4 plants. Orange, upregulated genes; blue, downregulated genes; green, non-DEGs with significant interactions with the network. Diamond shaped nodes, transcription factors. Main GO terms associated with clusters are highlighted. (F) Expression levels from RNA-seq of genes associated with SA biosynthesis in LO-LEC2 and RO-LEC2 plants compared to control (Ws-2/indLEC2) parent. Asterisks represent significant differences, determined by Wald test and adjusted with the Bonferroni–Holm method: ** p < 0.01, *** p < 0.001, (G) SA concentrations in leaves of LEC2 regenerants at the G3 generation. Asterisks represent significant differences, determined by Student’s t-test, ** p < 0.01, sample size of n = 10. Control = Ws-2/indLEC2 parent.

To determine what molecular changes might underpin the observed morphological variation, we performed whole-genome transcriptome analysis in leaves and roots from randomly selected, independent G3 lines. Using stringent thresholds [false discovery rate (FDR) <0.05; absolute log-two fold change >1.5], we obtained lists of Differentially Expressed Genes (DEGs) by comparing leaves and roots of regenerants and control plants ( S1 and S2 Tables). There were notable differences between the regenerants induced by the two embryonic transcription factors; leaves of RKD4-induced regenerants were the most affected independent of the tissue of origin (401 and 253 DEGs in leaves for LO and RO respectively, compared to 147 and 48 in roots). Notably, we found more DEGs for LO than for RO plants (Figs 2A and S2 ), which resembled the effects found in Col-0 plants cloned using RKD4 [ 12 ]. LEC2 regenerants had the highest numbers of DEGs in the opposite tissue from which the plant was regenerated, i.e., in roots of LO-LEC2 plants (282 DEGs versus 75 in leaves) and in leaves of RO-LEC2 plants (595 DEGs versus 61 in roots) (Figs 2A and S3 ). Since gene expression was strongly dysregulated in the leaves of both RO-RKD4 and RO-LEC2 regenerants, we looked for an overlap between the DEGs. We found more shared dysregulated genes than expected by chance (p-value = 2.1×10 −17 ), suggesting common effects independent of the regeneration strategy.

(A) Representative images of 28-day old Arabidopsis Ws-2 plants. Control (Ws-2/indLEC2), and clonal RO-LEC2 and LO-LEC2 G3 progeny. Scale bars, 5 cm. (B) Representative images of 28-day old Arabidopsis Ws-2 plants. Control (Ws-2/indRKD4), and clonal RO-RKD4 and LO-RKD4 G3 progeny. Scale bars, 5 cm. (C) Boxplot showing variation in plant biomass for control (indLEC2/Ws-2) and independent G3 lines. Asterisks represent significant differences, determined by Student’s t-test, ** p<0.01, *** p<0.001, sample size n = 10. (D) Violin plot and boxplot of leaf area for control (Ws-2/indLEC2) and independent G3 lines. Letters represent groups of statistically significantly different samples (p<0.05), determined by Tukey’s test, sample size n = 20.

In a previous study, we identified heritable molecular and phenotypic changes in Arabidopsis Col-0 plants propagated through the induction of the embryonic transcription factor RKD4 [ 12 ]. To better understand how this somaclonal variation is created, in particular the importance of the genetic background and/or the transcription factor employed, we generated clonal progeny from Arabidopsis Ws-2 leaf and root tissues using transgenic lines that allow the controlled expression of either RKD4 or LEC2, two transcription factor gene necessary for the initiation of different stages of embryo development [ 6 , 10 ]. To determine the stability of the phenotypes arising during cloning, we propagated seeds from each regenerated individual (G0) by selfing over three consecutive generations (G1-G3) under similar growth conditions, thus limiting possible effects caused by tissue culture. When we grew G2 and G3 clonal progeny, we noticed that the morphology of plants regenerated from roots using LEC ectopic expression (RO-LEC2) was noticeably different to control plants, while leaf regenerants (LO-LEC2) were indistinguishable from the control plants ( Fig 1A ). Notably, most RO-LEC2 lines (6/10) had reduced biomass, smaller leaf area and senesced early ( Fig 1C and 1D ), with different temperature growth conditions having no discernible effects on these phenotypes ( S1 Fig ). These phenotypes were only found in RO-LEC2 lines and plants regenerated using RKD4, either from root or leaf, did not produce any observable phenotypes. Collectively, our data suggest that the tissue of origin employed for regeneration and the regeneration protocol could contribute to phenotypic diversity in the clonal plants and their progenies, thus pointing to the long-term inheritance of somatic epigenetic states in the sexual progeny of clonal plants.

Discussion

A common concern surrounding clonal propagation in plants by tissue culture is the appearance of new undesirable phenotypes. This outcome may be in part attributed to the type of regeneration employed ie. organogenesis or somatic embryogenesis. For instance, using phytohormones is known to cause stochastic changes in DNA methylation, primarily hypomethylation, that are associated with changes in gene expression [11, 13, 16, 20, 21]. On the other hand, regeneration via somatic embryogenesis using embryonic transcription factors results in nonrandom changes in DNA methylation, which are heritable and associated with transcriptional and phenotypic variation [12]. To define the factor(s) that contribute to the molecular and phenotypic diversity found in plants propagated through somatic embryogenesis, we conducted a detailed analysis of regenerants created either by the ectopic expression of LEC2 or RKD4, two transcription factors that are part of distinct embryonic transcriptional networks [10, 20, 22]. Through this approach, we were able to identify heritable tissue-specific DNA methylation imprints in these regenerants that were associated with specific patterns of gene expression, leading to significant phenotypic variation. Notably, the molecular and phenotypic variation observed in clonal plants was independent of the transcription factor used for regeneration and instead strongly linked to the founder tissue employed.

The molecular mechanism(s) underpinning the inheritance of tissue-specific DNA methylation imprints that accumulate in these clonal plants are yet unknown, but they may be linked to the capacity of these two transcription factors to reprogram somatic cells such that they adopt an embryonic program without altering their epigenomic configuration. One explanation for this phenomenon could be that tissue-specific imprints arising during cloning are developmentally programmed, since leaves and roots have distinct epigenetic characteristics [23–27]. The tissue-specific imprints found in clonal plants may be linked to the distinct chromatin architecture found in root and shoot cells, which is largely influenced by chromatin loops associated with repressive histone marks [28]. Chromatin interactions likely contribute to the developmental differentiation of specific cell types in plants, as is the case in animals [29, 30], and it would be interesting to test if these interactions are maintained or reset in clonal plants. Nevertheless, our data show that some epigenetic imprints can be fixed independently of the pathway recruited to achieve somatic embryogenesis and regeneration. This suggests that genetic and epigenetic programs can be uncoupled in clonal plants.

Our data further show that irrespective of the transcription factor employed, plants regenerated from roots senesced early–a phenotype that was inherited by the progeny either after selfing or outcrossing. The observed early leaf senescence strongly correlated with DNA hypomethylation of specific TEs flanking genes associated with the SA pathway. Our data suggest that epimutations at TEs could accumulate in populations of species that reproduce asexually, and that these epimutations could confer an adaptive advantage under fluctuating environments. Several studies have shown that the long-distance regulatory action of TEs in Arabidopsis is associated with changes in DNA methylation [31]. Moreover, transposon mobilization and variation in TE methylation have been linked to environmental adaptation in natural plant populations [32] and that this epigenetic variation often occurs near genes associated with environmental responses [33, 34]. As such, the methylation of transposons has been selected to provide new regulatory functions in most eukaryotic genomes [35].

The SA pathway may be an important target for the accumulation of epimutations in plants, as it is critical for defense [36], and is strongly correlated with biomass, a characteristic that has traditionally been selected by breeders to increase yield in various crops, including maize [37], rice [38], and wheat [39]. Notably, mutants that cause a global change in chromatin organization, such as CROWDED NUCLEI (CRWN), display constitutive activity of the salicylic acid-dependent pathway of immunity, with crwn plants displaying dwarfism and premature senescence [40, 41].

Epigenetic imprints generated during cloning can be inherited over multiple cycles of sexual reproduction, suggesting that the epigenetic machinery in plants is unable to repair these epimutations [11, 12, 16]. The stable accumulation of epimutations has also been documented in crosses between wild-type plants and mutants defective in DNA methylation [42–46] and histone demethylation [47]. Notably, while the tissue-specific DNA hypomethylation imprints of clonal plants are transmitted through both the maternal and paternal germline to the offspring. However, DNA hypermethylation imprints are only transmitted maternally. The molecular mechanisms implicated in the resetting of these DNA hypermethylated imprints are not yet known but may be linked to the active epigenomic reprogramming that takes place during male gametogenesis [48, 49] and/or embryo development [50]. Nevertheless, our study reveals that the parental transmission of the epigenetic imprints generated during clonal propagation could be used as a means of controlling their maintenance or erasure in plant breeding.

In summary, our study has revealed that clonal propagation via somatic embryogenesis using embryonic transcription factors enables the generation of specific epigenomic changes leading to regenerated plants with novel phenotypes. Moreover, because these epigenomic changes are stable albeit exhibit selection/bias during sexual reproduction, stable epimutations could arise and be maintained in populations of plants that alternate between asexual and sexual programs.

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