Epigenetic Basis of Morphological Variation and Phenotypic Plasticity inArabidopsis thaliana

Abstract

Epigenetics is receiving growing attention in the plant science community. Epigenetic modifications are thought to play a particularly important role in fluctuating environments. It is hypothesized that epigenetics contributes to plant phenotypic plasticity because epigenetic modifications, in contrast to DNA sequence variation, are more likely to be reversible. The population of decrease in DNA methylation 1-2 (ddm1-2)-derived epigenetic recombinant inbred lines (epiRILs) in Arabidopsis thaliana is well suited for studying this hypothesis, as DNA methylation differences are maximized and DNA sequence variation is minimized. Here, we report on the extensive heritable epigenetic variation in plant growth and morphology in neutral and saline conditions detected among the epiRILs. Plant performance, in terms of branching and leaf area, was both reduced and enhanced by different quantitative trait loci (QTLs) in the ddm1-2 inherited epigenotypes. The variation in plasticity associated significantly with certain genomic regions in which the ddm1-2 inherited epigenotypes caused an increased sensitivity to environmental changes, probably due to impaired genetic regulation in the epiRILs. Many of the QTLs for morphology and plasticity overlapped, suggesting major pleiotropic effects. These findings indicate that epigenetics contributes substantially to variation in plant growth, morphology, and plasticity, especially under stress conditions.

Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphological Traits in Arabidopsis

“…Similar to the problem of missing heritability in human GWA studies, where individual variants cannot explain the phenotypic variation despite high heritabilities (Yang et al, 2010;Gibson, 2011;Makowsky et al, 2011), genetic variants cannot fully explain the high heritabilities in plant studies (Brachi et al, 2010;Sasaki et al, 2015). Several reasons, such as population structure (Filiault and Maloof, 2012), epistasis (Chan et al, 2011;Brachi et al, 2015;Kruijer, 2016), GxE (Sasaki et al, 2015), epigenetics (Johannes et al, 2009;Kooke et al, 2015), sample size (Korte and Farlow, 2013), heterogeneity (Atwell et al, 2010;Barboza et al, 2013), rare alleles (Salomé et al, 2011;Sanchez-Bermajo et al, 2015), and a high number of small-effect loci (Joseph et al, 2013;Verslues et al, 2014) can complicate the association between polymorphisms and phenotypes.…”

“…Plant performance is directly determined by life history traits, such as flowering time and growth rate, which in turn depend on genetics, morphology, physiology, and the environment (Roff, 2007;Kooke et al, 2015). Understanding the regulation of plant growth and morphology is therefore essential for the comprehension of plant performance.…”

Genetic divergence between Mexican Opuntia accessions inferred by polymerase chain reaction-restriction fragment length polymorphism analysis

“…Similarly, epigenetic molecular phenomena are capable of altering the temporal, spatial, and abundance patterns of gene expression. These modifications may have morphological, physiological, and ecological consequences, and are heritable across generations (Kooke et al, 2015). The study of natural epigenetic variation is complicated due to the large contribution of DNA sequence variation compared to phenotypic variation within species.…”

Epigenetic variation contributes to environmental adaptation of Arabidopsis thaliana

“…4 Recent work in Arabidopsis shows that the phenotypic variation between epi-RILs, introduced by DNA-methylation differences, is highly heritable and differs between environments. 5 Epigenetic modifications might, therefore, serve as an important resource for adaptation to changing environments. 6 In support of the original paper 5 we summarize the major findings and reanalyzed the data for further clarification.…”

“…5 Epigenetic modifications might, therefore, serve as an important resource for adaptation to changing environments. 6 In support of the original paper 5 we summarize the major findings and reanalyzed the data for further clarification. Specifically, we quantified the amount of observed variation in trait values in the epi-RIL population and estimated the partition of variation into epigenetic and other factors.…”