Research

Extending the Modern Synthesis

The Modern Synthesis fused Mendelian genetics and Darwinian evolution to provide a unified theory of evolution [1]. Heritable, genetic changes that contribute to phenotypic differences between individuals of a population are the foundations of the Modern Synthesis. However, epigenetics, the molecular mechanism of heritable gene expression changes that cannot be attributed to changes in DNA sequence information, potentially offers an alternative path for evolution [2]. Unlike epigenetics, which implies the mechanism, the epigenome, which includes all post-translational modifications and other chromatin features associated with regulatory elements in the genome, potentially provides the substrate for evolution [2]. Indeed, the generation of epialleles through natural and induced sources has given rise to novel phenotypic variation, ranging from altered disease resistance, variation in biomass, oil yield, and flower morphology within a population (Fig. 1) [3–6]. I am interested in how epigenetics and the epigenome fits within the Modern Synthesis.

Figure 1. An epigenetic mutation responsible for natural variation in floral symmetry in Linaria vulgaris (toadflax) [3]. The Lcyc gene is methylated and transcriptionally silent in the peloric mutant. This epiallele co-segregates with the mutant phenotype. Figure modified from [3].

The evolutionary origins and function of epigenomic variation

Sparse sampling of DNA and histone modifications, and taxonomic groups hinder our understanding of the evolutionary origins and function of epigenomic variation. Furthermore, explanations for the observed patterns of 5-methylcytosine (5mC) – the most well studied type of epigenomic variation – and its functional importance, remain largely unknown [7–11] (Fig. 2). It is only through strengthening our understanding of the evolution of genetic mechanisms that establish and maintain DNA and histone modifications, genome evolution, life history, and modification crosstalk can we develop a comprehensive theory for the origins and function of epigenomic variation. I am interested in pairing comparative methods with functional genetics to test hypotheses for the evolutionary origins and function of epigenomic variation.

cg_methylation.plants.bw.landscape_10062

Figure 2. Epigenomic variation across Chlorophyta and within Arabidopsis thaliana.

Epigenome editing for crop improvement

The epigenome harnesses the potential for crop improvement without perturbing established genetic associations. Work in the model plant Arabidopsis thaliana has radically changed our perception of the epigenomic contributions to complex phenotypic traits [11]. Furthermore, the development of promising new methodologies for engineering 5mC states in a site-specific manner in plant genomes make testing the effect of epialleles on phenotypic traits possible [12]. A limiting step in epigenome editing for crop improvement is the identification of epialleles that are linked to phenotypic variation (Fig. 1). Much like the identification of genetic variation for crop improvement, looking to naturally occurring epigenomic variation provides an endless source of epialleles (Fig. 3). Thus, I am interested in unlocking the epigenome for crop improvement through the identification of epialleles that contribute to morphological variation within wild populations.

Figure 3. Discovery of epialleles under selection using population genetics. (A) Identification of polymorphic methylated cytosines and epialleles within a population. (B) Epiallele frequency spectrum provides information on demographic changes and natural selection. (C) Tajima's D – a comparison of the average number of pairwise differences with the number of segregating sites can distinguish between epialleles evolving neutrally and on evolving under a non-random process (i.e., selective sweep) relative to a genetic alleles.

References

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