Genotypic variation in the persistence of transgenerational responses to seasonal cues

Environment-induced heritable variations are common in Arabidopsis thaliana

Parental or ancestral environments can induce heritable phenotypic changes, but whether such environment-induced heritable changes are a common phenomenon remains unexplored. Here, we subject 14 genotypes of Arabidopsis thaliana to 10 different environmental treatments and observe phenotypic and genome-wide gene expression changes over four successive generations. We find that all treatments caused heritable phenotypic and gene expression changes, with a substantial proportion stably transmitted over all observed generations. Intriguingly, the susceptibility of a genotype to environmental inductions could be predicted based on the transposon abundance in the genome. Our study thus challenges the classic view that the environment only participates in the selection of heritable variation and suggests that the environment can play a significant role in generating of heritable variations.

Variation and plasticity in life-history traits and fitness of wild Arabidopsis thaliana populations are not related to their genotypic and ecological diversity

BACKGROUND

Despite its implications for population dynamics and evolution, the relationship between genetic and phenotypic variation in wild populations remains unclear. Here, we estimated variation and plasticity in life-history traits and fitness of the annual plant Arabidopsis thaliana in two common garden experiments that differed in environmental conditions. We used up to 306 maternal inbred lines from six Iberian populations characterized by low and high genotypic (based on whole-genome sequences) and ecological (vegetation type) diversity.

RESULTS

Low and high genotypic and ecological diversity was found in edge and core Iberian environments, respectively. Given that selection is expected to be stronger in edge environments and that ecological diversity may enhance both phenotypic variation and plasticity, we expected genotypic diversity to be positively associated with phenotypic variation and plasticity. However, maternal lines, irrespective of the genotypic and ecological diversity of their population of origin, exhibited a substantial amount of phenotypic variation and plasticity for all traits. Furthermore, all populations harbored maternal lines with canalization (robustness) or sensitivity in response to harsher environmental conditions in one of the two experiments.

CONCLUSIONS

Overall, we conclude that the environmental attributes of each population probably determine their genotypic diversity, but all populations maintain substantial phenotypic variation and plasticity for all traits, which represents an asset to endure in changing environments.

Non-stressful temperature changes affect transgenerational phenotypic plasticity across the life cycle of Arabidopsis thaliana plants

BACKGROUND AND AIMS

Plants respond in a plastic manner to seasonal changes, often resulting in adaptation to environmental variation. Although much is known about how seasonality regulates developmental transitions within generations, transgenerational effects of non-stressful environmental changes are only beginning to be unveiled. This study aimed to evaluate the effects of ambient temperature changes on the expression of transgenerational plasticity in key developmental traits of Arabidopsis thaliana plants.

METHODS

We grew Columbia-0 plants in two contrasting temperature environments (18 and 24 °C) during their whole life cycles, or the combination of those temperatures before and after bolting (18-24 and 24-18 °C) across two generations. We recorded seed germination, flowering time and reproductive biomass production for the second generation, and seed size of the third generation.

KEY RESULTS

The environment during the whole life cycle of the first generation of plants, even that experienced before flowering, influenced the germination response and flowering time of the second generation. These effects showed opposing directions in a pattern dependent on the life stage experiencing the cue in the first generation. In contrast, the production of reproductive biomass depended on the immediate environment of the progeny generation. Finally, the seed area of the third generation was influenced positively by correlated environments across generations.

CONCLUSIONS

Our results suggest that non-stressful environmental changes affect the expression of key developmental traits across generations, although those changes can have contrasting effects depending on the parental and grandparental life stage that perceives the cue. Thus, transgenerational effects in response to non-stressful cues might influence the expression of life-history traits and potential adaptation of future generations.

Plant environmental memory: implications, mechanisms and opportunities for plant scientists and beyond

Plants are extremely plastic organisms. They continuously receive and integrate environmental information and adjust their growth and development to favour fitness and survival. When this integration of information affects subsequent life stages or the development of subsequent generations, it can be considered an environmental memory. Thus, plant memory is a relevant mechanism by which plants respond adaptively to different environments. If the cost of maintaining the response is offset by its benefits, it may influence evolutionary trajectories. As such, plant memory has a sophisticated underlying molecular mechanism with multiple components and layers. Nonetheless, when mathematical modelling is combined with knowledge of ecological, physiological, and developmental effects as well as molecular mechanisms as a tool for understanding plant memory, the combined potential becomes unfathomable for the management of plant communities in natural and agricultural ecosystems. In this review, we summarize recent advances in the understanding of plant memory, discuss the ecological requirements for its evolution, outline the multilayered molecular network and mechanisms required for accurate and fail-proof plant responses to variable environments, point out the direct involvement of the plant metabolism and discuss the tremendous potential of various types of models to further our understanding of the plant's environmental memory. Throughout, we emphasize the use of plant memory as a tool to unlock the secrets of the natural world.

Plastic maternal effects of social density on reproduction and fitness in the least killifish, Heterandria formosa

Environmental parental effects, also known as transgenerational plasticity, are widespread in plants and animals. Less well known is whether those effects contribute to maternal fitness in the same manner in different populations. We carried out a multigenerational laboratory experiment with females drawn from two populations of the least killifish, Heterandria formosa, to assess transgenerational plasticity in reproductive traits in response to differences in social density and its effects on maternal fitness. In the first and second generations, increased density decreased reproductive rate and increased offspring size in females from both populations. There were complicated patterns of transgenerational plasticity on maternal fitness that differed between females from different populations. Females from a population with historically low densities whose mothers experienced lower density had higher fitness than females whose mothers experienced higher density, regardless of their own density. The opposite pattern emerged in females from the population with historically high densities: Females whose mothers experienced higher density had higher fitness than females whose mothers experienced lower density. This transgenerational plasticity is not anticipatory but might be considered adaptive in both populations if providing those "silver spoons" enhances offspring fitness in all environments.

Transgenerational effects of temperature fluctuations in Arabidopsis thaliana

Plant stress responses can extend into the following generations, a phenomenon called transgenerational effects. Heat stress, in particular, is known to affect plant offspring, but we do not know to what extent these effects depend on the temporal patterns of the stress, and whether transgenerational responses are adaptive and genetically variable within species. To address these questions, we carried out a two-generation experiment with nine Arabidopsis thaliana genotypes. We subjected the plants to heat stress regimes that varied in timing and frequency, but not in mean temperature, and we then grew the offspring of these plants under controlled conditions as well as under renewed heat stress. The stress treatments significantly carried over to the offspring generation, with timing having stronger effects on plant phenotypes than stress frequency. However, there was no evidence that transgenerational effects were adaptive. The magnitudes of transgenerational effects differed substantially among genotypes, and for some traits the strength of plant responses was significantly associated with the climatic variability at the sites of origin. In summary, timing of heat stress not only directly affects plants, but it can also cause transgenerational effects on offspring phenotypes. Genetic variation in transgenerational effects, as well as correlations between transgenerational effects and climatic variability, indicates that transgenerational effects can evolve, and have probably already done so in the past.

Dormant plasticity of rotifer diapausing eggs in response to predator kairomones

In freshwater ecosystems, hatching strategy of diapausing eggs (DEs) under predation risk has important ecological implication for zooplankters. Although kairomones released by predators can induce phenotypic responses of prey, hatching patterns of DEs in response to kairomones have received contradictory conclusions in zooplankters. Maternal environment may also affect hatching strategy of DEs during predator-prey interactions. We used classical Brachionus calyciflorus-Asplanchna models to determine the timing and proportion of DE hatching in association with parental and embryonic exposure to kairomones. Results obtained from two Brachionus clones supported the hypothesis that DEs could detect Asplanchna kairomones and adjust hatching patterns. DEs showed early and synchronous hatching patterns in the environment with kairomones. Data also supported the prediction that DEs could gain information about predators from maternal environments and adjusted their hatching pattern in response to the presence of kairomones. Compared with DEs from Brachionus mothers not exposed to kairomones, DEs produced by mothers that were experienced with kairomones attained a higher hatching rate when both of them hatched in the environment either with or without kairomones. Our results suggest that DEs of B. calyciflorus possess dormant plasticity to defend against predation from Asplanchna, which may be regulated by maternal environmental effects during sexual life cycles.

Genetic differences in the temporal and environmental stability of transgenerational environmental effects

Environments influence the expression of phenotypes of individuals, their progeny, and even their grandprogeny. The duration of environmental effects and how they are modified by subsequent environments are predicted to be targets of natural selection in variable environments. However, little is known about the genetic basis of the temporal persistence of environmental effects and their stability of expression across subsequent environments, or even the extent to which natural genotypes differ in these attributes of environmental effects. We factorially manipulated the thermal environment experienced in three successive generations, to quantify the temporal persistence and environmental stability of temperature effects in contrasting genotypes of Arabidopsis thaliana. We found that genotypes differed in the manner in which environmental effects dissipated across successive generations, the manner in which responses to ancestral environments were stably expressed in present environments, the manner in which ancestral environments altered responses to present environments, and in the manner in which ancestral environments altered fitness in present conditions. Genetic variation exists in nature for these trait-specific environmental responses, suggesting that the temporal persistence and stability of environmental effects in variable environments have the potential to evolve in response to natural selection imposed by different environments and sequences of environments.

Transgenerational effects of parent plant competition on offspring development in contrasting conditions

Conditions during a parent's lifetime can induce phenotypic changes in offspring, providing a potentially important source of variation in natural populations. Yet, to date, biotic factors have seldom been tested as sources of transgenerational effects in plants. In a greenhouse experiment with the generalist annual Polygonum persicaria, we tested for effects of parental competition on offspring by growing isogenic parent plants either individually or in competitive arrays and comparing their seedling progeny in contrasting growth environments. Offspring of competing vs. non-competing parents showed significantly altered development, resulting in greater biomass and total leaf area, but only when growing in neighbor or simulated canopy shade, rather than sunny dry conditions. A follow-up experiment in which parent plants instead competed in dry soil found that offspring in dry soil had slightly reduced growth, both with and without competitors. In neither experiment were effects of parental competition explained by changes in seed provisioning, suggesting a more complex mode of regulatory inheritance. We hypothesize that parental competition in moist soil (i.e., primarily for light) confers specific developmental effects that are beneficial for light-limited offspring, while parental competition in dry soil (i.e., primarily for belowground resources) produces offspring of slightly lower overall quality. Together, these results indicate that competitive conditions during the parental generation can contribute significantly to offspring variation, but these transgenerational effects will depend on the abiotic resources available to both parents and progeny.

Transgenerational non-genetic inheritance has fitness costs and benefits under recurring stress in the clonal duckweed Spirodela polyrhiza

Although non-genetic inheritance is thought to play an important role in plant ecology and evolution, evidence for adaptive transgenerational plasticity is scarce. Here, we investigated the consequences of copper excess on offspring defences and fitness under recurring stress in the duckweed Spirodela polyrhiza across multiple asexual generations. Growing large monoclonal populations (greater than 10 000 individuals) for 30 generations under copper excess had negative fitness effects after short and no fitness effect after prolonged growth under recurring stress. These time-dependent growth rates were likely influenced by environment-induced transgenerational responses, as propagating plants as single descendants for 2 to 10 generations under copper excess had positive, negative or neutral effects on offspring fitness depending on the interval between initial and recurring stress (5 to 15 generations). Fitness benefits under recurring stress were independent of flavonoid accumulations, which in turn were associated with altered plant copper concentrations. Copper excess modified offspring fitness under recurring stress in a genotype-specific manner, and increasing the interval between initial and recurring stress reversed these genotype-specific fitness effects. Taken together, these data demonstrate time- and genotype-dependent adaptive and non-adaptive transgenerational responses under recurring stress, which suggests that non-genetic inheritance alters the evolutionary trajectory of clonal plant lineages in fluctuating environments.

How is epigenetics predicted to contribute to climate change adaptation? What evidence do we need?

Transgenerational effects that are interpreted in terms of epigenetics have become an important research focus at a time when rapid environmental changes are occurring. These effects are usually interpreted as enhancing fitness extremely rapidly, without depending on the slower process of natural selection changing DNA-encoded (fixed) genetic variants in populations. Supporting evidence comes from a variety of sources, including environmental associations with epialleles, cross-generation responses of clonal material exposed to different environmental conditions, and altered patterns of methylation or frequency changes in epialleles across time. Transgenerational environmental effects have been postulated to be larger than those associated with DNA-encoded genetic changes, based on (for instance) stronger associations between epialleles and environmental conditions. Yet environmental associations for fixed genetic differences may always be weak under polygenic models where multiple combinations of alleles can lead to the same evolutionary outcome. The ultimate currency of adaptation is fitness, and few transgenerational studies have robustly determined fitness effects, particularly when compared to fixed genetic variants. Not all transgenerational modifications triggered by climate change will increase fitness: stressful conditions often trigger negative fitness effects across generations that can eliminate benefits. Epigenetic responses and other transgenerational effects will undoubtedly play a role in climate change adaptation, but further, well-designed, studies are required to test their importance relative to DNA-encoded changes. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'

Ecological, (epi)genetic and physiological aspects of bet-hedging in angiosperms

KEY MESSAGE

Bet-hedging is a complex evolutionary strategy involving morphological, eco-physiological, (epi)genetic and population dynamics aspects. We review these aspects in flowering plants and propose further research needed for this topic. Bet-hedging is an evolutionary strategy that reduces the temporal variance in fitness at the expense of a lowered arithmetic mean fitness. It has evolved in organisms subjected to variable cues from the external environment, be they abiotic or biotic stresses such as irregular rainfall or predation. In flowering plants, bet-hedging is exhibited by hundreds of species and is mainly exerted by reproductive organs, in particular seeds but also embryos and fruits. The main example of bet-hedging in angiosperms is diaspore heteromorphism in which the same individual produces different seed/fruit morphs in terms of morphology, dormancy, eco-physiology and/or tolerance to biotic and abiotic stresses in order to 'hedge its bets' in unpredictable environments. The objective of this review is to provide a comprehensive overview of the ecological, genetic, epigenetic and physiological aspects involved in shaping bet-hedging strategies, and how these can affect population dynamics. We identify several open research questions about bet-hedging strategies in plants: 1) understanding ecological trade-offs among different traits; 2) producing more comprehensive phylogenetic analyses to understand the diffusion and evolutionary implications of this strategy; 3) clarifying epigenetic mechanisms related to bet-hedging and plant responses to environmental cues; and 4) applying multi-omics approaches to study bet-hedging at different levels of detail. Clarifying those aspects of bet-hedging will deepen our understanding of this fascinating evolutionary strategy.

Mimulus sRNAs Are Wound Responsive and Associated with Transgenerationally Plastic Genes but Rarely Both

Organisms alter development in response to environmental cues. Recent studies demonstrate that they can transmit this plasticity to progeny. While the phenotypic and transcriptomic evidence for this “transgenerational plasticity” has accumulated, genetic and developmental mechanisms remain unclear. Plant defenses, gene expression and DNA methylation are modified as an outcome of parental wounding in Mimulus guttatus. Here, we sequenced M. guttatus small RNAs (sRNA) to test their possible role in mediating transgenerational plasticity. We sequenced sRNA populations of leaf-wounded and control plants at 1 h and 72 h after damage and from progeny of wounded and control parents. This allowed us to test three components of an a priori model of sRNA mediated transgenerational plasticity—(1) A subset of sRNAs will be differentially expressed in response to wounding, (2) these will be associated with previously identified differentially expressed genes and differentially methylated regions and (3) changes in sRNA abundance in wounded plants will be predictive of sRNA abundance, DNA methylation, and/or gene expression shifts in the following generation. Supporting (1) and (2), we found significantly different sRNA abundances in wounded leaves; the majority were associated with tRNA fragments (tRFs) rather than small-interfering RNAs (siRNA). However, siRNAs responding to leaf wounding point to Jasmonic Acid mediated responses in this system. We found that different sRNA classes were associated with regions of the genome previously found to be differentially expressed or methylated in progeny of wounded plants. Evidence for (3) was mixed. We found that non-dicer sRNAs with increased abundance in response to wounding tended to be nearby genes with decreased expression in the next generation. Counter to expectations, we did not find that siRNA responses to wounding were associated with gene expression or methylation changes in the next generation and within plant and transgenerational sRNA plasticity were negatively correlated.

Digest: Transgenerational stress memory mechanisms in Arabidopsis thaliana

Arabidopsis thaliana accessions have shown genetic diversity and type of stressor to be important determinants of transgenerational stress memory. Alvarez et al. found that certain accessions showed reversible phenotypic plasticity, supporting a model of transgenerational stress memory based upon epigenetic changes. The main proposed epigenetic regulators include DNA methylation, histone modifications, and RNA silencing via small noncoding RNA.