Assignment 1

This web page was produced as an assignment for an undergraduate course at Davidson College.

Image courtesy of David Landscape Architecture

1) What was the research project?

A 2016 study conducted by researchers at Wesleyan University and published in the Journal of the Royal Society examined whether methylation modifications contribute to the transgenerational plasciticy of Polygonum persicaria in response to parental drought stress by comparing the growth of progeny from drought-stressing versus moist parental environments and exposure to the demethylating agent zebularine versus control conditions. (Sultan, Herman, 2016) By comparing the biomass and root length of progeny produced by self-fertilization when grown in dry soil, the authors calculated the effects of the parental environment, exposure to the demethylation agent during seed germination, and genetic lineage via linear mixed-effect models. This would provide further insight into the contribution and prevalence of epigenetic modifications to the transgenerational plasticity of plant species. They found that progeny of plants grown in moist conditions showed similar growth regardless of treatment in dry soil, but among progeny of plants grown in the drought environment, seeds germinated in control conditions outgrew those exposed to the zebularine during germination.

2) Were they testing a hypothesis or doing discovery science?

The authors were testing the hypothesis that methylation modifications contribute to the previously documented transgenerational plasticity of Polygonum persicaria in response to drought conditions. (Herman et al, 2011) They were testing whether exposure to the demethylating agent during seed germination would inhibit growth of progeny from a drought-like parental environment when compared to progeny derived from plants grown in a moist parental environment.

3) What genomic technology was used in the project?

The genomic effects of methylation on transgenerational plasticity were measured indirectly from the average estimated biomass of seedlings (calculated as the sum of their root and shoot biomass), the total root length, and the leaf area (extrapolated from the first three true leaves of each seedling) The length of root systems washed free of soil were measured with a Comair optical scanner. The first three true leaves were scanned on a LI-3100 leaf area meter, dried, and then weighed to estimate specific leaf area (leaf surface area per unit mass; cm2 leaf/g leaf). Zebularine was used as the demethylation agent, and seeds were germinated on 0.8% agar petri dishes containing either 0 or 45 mM zebularine.

4) What was the take home message?

Among twelve genetic lines drawn from distinct natural populations and propagated by self-fertilization for five generations, progeny from the moist parental environment demonstrated comparable growth regardless of exposure to zebularine, but seeds germinated in control conditions exhibited significantly superior seedling biomass, root length, and leaf area among the progeny of the drought-stressing parental environment. These results convincingly indicate the specific contribution of methylation to transgenerational plasticity in response to drought-stressing conditions, and their inhibition by zebularine.

Fig. 1.
Validation of demethylation-driven inhibition of growth indicated by changes in total root length (a), leaf area (b) and biomass (c), in comparison of progeny from moist or drought-like parental conditions. Asterisks indicate significance of parental drought effect through one-way ANOVA separately testing effect of parents environment on both exposure groups.
(replicated Herman and Sultan, 2016)

Table 1.
Effects of parental environment, germination treatment, and genetic line and the observed interactions of these factors with phenotypic changes. The variance for each random effect is expressed as the percentage of the variance that was unexplained by fixed effects, with the genetic line and its interactions treated as random effects (random effect variance/(sum of all random effect variances þ residual variance). Genetic lines were found to vary in both the effect of parental drought and its alteration by demethylation. Seed provisioning was included as a covariate, and spatial block was included as a fixed effect. (replicated Herman and Sultan, 2016)

These findings support the authors’ hypothesis that the drought-related transgenerational plasticity seen in Polygonum persicaria is attributable to methylation changes operating outside traditional Mendelian inheritance in as little time as a single generation, while also demonstrating distinctions in response to demethylation among the genetic lines sample.The results fall in line with a number of studies documenting transgenerational plasticity in other plant species like Maritime pine trees.

5) What is your evaluation of the project?

This study continues to reshape our understanding of the non-mendelian forces contributing to evolution, and the incredibly short time in which epigenetic modifications can be passed on to offspring resulting from parental exposure. It has broader implications for inheritance and short term, population-wide evolution in the face of rapidly shifting environments, which has became an increasingly common topic of public-oriented discussion. For example, in their book Evolving Ourselves, Futurist Juan Enriquez and geneticist Steve Gullans point to the 78% increase in the likelihood of autism from 2000 to 2008, and its decrease in genetic predictability from between 80 and 90% to only 50%, as one illustration of the “unnatural selection” and “nonrandom mutation” currently driving short-term evolutionary trends (Enriquez and Gullans 2015). This trend simultaneously toughens the task undertaken by genomic diagnostic companies such as 23andme, and increases uncertainty surrounding how our environment or diet may be driving our own evolution.

It also more positively suggests that certain plant species may react better than anticipated to climate change, especially if selection for such modifications developed among ancestors exposed to more dynamic environments has been conserved and passed down over many generations. If particular crop strains demonstrated such characteristics, their wider use might crucially benefit food security as climate change continues to drastically alter weather patterns.

Scientific Evaluation:

The genetic diversity of tested samples and consistently inferior growth of zebularine-treated seeds among progeny of the drought-stressing parental environment seems to establish that demethylation disrupts the transgenerational plasticity of Polygonum persicaria, confirming the hypothesis of Herman and Sultan. The specific effects of the parental environment, genetic line, and germination treatment as calculated by the authors’ linear mixed-effects models, however, raises questions regarding the design of these models. While it was noted that genetic lines altered to varying degrees in response to parental drought stress, it was not explained whether the climate of the area from which specific genetic lines were derived showed overarching similarities in their response to drought stress. Whether lines derived from more commonly drought-stressed ecosystems showed heightened transgenerational plasticity in comparison to lines from populations in more moderate environments was not indicated. Sequencing of the transcriptome or whole genome of seedlings from each area could have provided highly illuminating information on the baseline differences in gene expression of different genetic lines. Further, such sequencing could potentially elucidate the specific basis of epigenetic mechanisms that act in response to drought conditions, and whether a pattern of their modification exists across specific chromosomal domains and haplotypes versus specific genes.

References:

Herman, Jacob J., and Sonia E. Sultan. 2016. “DNA Methylation Mediates Genetic Variation for Adaptive Transgenerational Plasticity.” Proc. R. Soc. B 283 (1838): 20160988. doi:10.1098/rspb.2016.0988.

Herman, Jacob J., Sonia E. Sultan, Tim Horgan-Kobelski, and Charlotte Riggs. 2012. “Adaptive Transgenerational Plasticity in an Annual Plant: Grandparental and Parental Drought Stress Enhance Performance of Seedlings in Dry Soil.” Integrative and Comparative Biology 52 (1): 77–88. doi:10.1093/icb/ics041.

Enriquez, Juan, and Steve Gullans. 2015. Evolving Ourselves : How Unnatural Selection and Nonrandom Mutation Are Changing Life on Earth. New York, New York: Current. http://catdir.loc.gov/catdir/enhancements/fy1516/2014451987-s.html.

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