Phenotypic effects

Single locus epigenetic effects on phenotype

The ultimate requirement for DNA methylation variation to be adaptive, in addition to being stable and not under genetic control, is to have phenotypic relevance. There are several examples of phenotypic effects of epigenetic marks, from heterophylly (Herrera and Bazaga 2013) to stress responses (Kinoshita and Seki 2014) and others, but only few meet the requirements of being stable and “pure”, i.e. not under genetic control. Although rare, there are few examples of pure naturally occurring epimutations at a single locus which cause mutant phenotypes. The most famous example is the peloric mutant of Lynaria vulgaris, in which spontaneous DNA methylation of the Lcyc gene promoter drives a change in flower symmetry from bilateral to radial (Cubas, Vincent, and Coen 1999). Such a phenotype can be transmitted to the next generation and can sometimes revert back to WT during somatic development. This can sometimes result in branches of peloric and WT flowers originating from the same plant, confirming that the Lcyc promoter methylation is pure and not genetically controlled. A second striking example is the naturally occurring hypermethylation of the Colorless non-ripening (Cnr) gene promoter, inhibiting fruit ripening in Tomato (Manning et al. 2006). This epimutation is even more stable than the Lynaria case, as the fruit phenotype only very rarely reverts to WT. Other examples of epialleles were described in few more plant species, some naturally occurring and some resulting from induced mutagenesis. Some examples were listed by (Kalisz and Purugganan 2004) and few cases confidently exclude any chance of genetic control of the described epimutations.

Figure 4: Examples of single locus phenotypic effects of DNA methylation epialleles. WT phenotype is at the top while mutant phenotype at the bottom for A) tomato (Manning et al. 2006), B) Linaria vulgaris (Cubas et al. 1999), and C) oil palm (Ong-Abdulla et al. 2015).

Epigenetic effects on complex traits

Although single locus epialleles are undoubtedly rare, most plant traits are polygenic. Therefore, more insights into epigenetic effects on complex traits are required to understand the potential of epigenetic contribution to plant adaptation. Unfortunately, such studies are so technically difficult that they are basically nonexistent. Showing causation of a single epimutation with a clear phenotype is already a hard task, doing so for putative epigenetic variants controlling quantitative traits is even harder. The only studies that have tackled this challenge and successfully identified DNA methylation variants affecting quantitative traits, so called epiQTLs, made use of A. thaliana epigenetic recombinant inbred lines epiRILs (Cortijo et al. 2014; Furci et al. 2019). Because this population harbours random DNA methylation variation in a uniform genetic background, any heritable phenotypic effect can be directly attributed to the methylation variation. Using this system Cortijo et al. 2014 managed to identify Differentially Methylated Regions explaining 60% to 90% of the flowering time and primary root length variation observed. More recently, hypomethylated DNA loci controlling quantitative resistance to the fungal pathogen Hyaloperonospora arabidopsidis to were also identified in the epiRILs (Furci et al. 2019).