Plasticity across levels: relating epigenomic, transcriptomic, and phenotypic responses to osmotic stress in a halotolerant microalga

Phenotypic plasticity, the ability of a given genotype to produce
alternative phenotypes in response to its environment of development, is
an important mechanism for coping with variable environments. While the
mechanisms underlying phenotypic plasticity are diverse, their relative
contributions need to be investigated quantitatively to better understand
the evolvability of plasticity across biological levels. This requires
relating plastic responses of the epigenome, transcriptome, and organismal
phenotype, and investigating how they vary with the genotype. Here we
carried out this approach for responses to osmotic stress in Dunaliella
salina, a green microalga that is a model organism for salinity tolerance.
We compared two strains that show markedly different demographic responses
to osmotic stress, and showed that these phenotypic responses involve
strain- and environment-specific variation in gene expression levels, but
a relative low - albeit significant - effect of strain × environment
interaction. We also found an important genotype effect on the genome-wide
methylation pattern, but little contribution from environmental conditions
to the latter. However, we did detect a significant marginal effect of
epigenetic variation on gene expression, beyond the influence of genetic
differences on epigenetic state, and we showed that hypomethylated regions
are correlated with higher gene expression. Our results indicate that
epigenetic mechanisms are either not involved in the rapid plastic
response to environmental change in this species, or involve only few
changes in trans that are sufficient to trigger concerted changes in the
expression of many genes, and phenotypic responses by multiple traits.