The Pea (Pisum sativum L.) Rogue Paramutation is Accompanied by Alterations in the Methylation Pattern of Specific Genomic Sequences

Mendelian and non-Mendelian genetics in model plants

The "Mendelian Rules" of inheritance are cornerstones of genetics, described in Mendel's seminal publication from 1866. The experimental results and their interpretation have been discussed in numerous ways. This perspective emphasizes the contribution of Mendel's preparations prior to his crossing experiments to the discovery of Mendelian genetics. This thoughtful experimental design, and some fortune, avoided pitfalls that could have resulted in non-Mendelian inheritance.

A Non-Rogue Mutant Line Induced by ENU Mutagenesis in Paramutated Rogue Peas (Pisum sativum L.) Is Still Sensitive to the Rogue Paramutation

The spontaneously emerging rogue phenotype in peas (Pisum sativum L.), characterized by narrow and pointed leaf stipula and leaflets, was the first identified case of the epigenetic phenomenon paramutation. The crosses of homozygous or heterozygous (e.g., F1) rogue plants with non-rogue (wild type) plants, produce exclusively rogue plants in the first and all subsequent generations. The fact that the wild phenotype disappears forever, is in clear contradiction with the Mendelian rules of inheritance, a situation that impedes the positional cloning of genes involved in this epigenetic phenomenon. One way of overcoming this obstacle is the identification of plant genotypes harboring naturally occurring or artificially induced neutral alleles, non-sensitive to paramutation. So far, such alleles have never been described for the pea rogue paramutation. Here, we report the induction via 1-ethyl-1-nitrosourea (ENU) mutagenesis of a non-rogue revertant mutant in the rogue cv. Progreta, and the completely unusual fixation of the induced non-rogue phenotype through several generations. The reversion of the methylation status of two previously identified differentially methylated genomic sequences in the induced non-rogue mutant, confirms that the rogue paramutation is accompanied by alterations in DNA methylation. Nevertheless, unexpectedly, the induced non-rogue mutant showed to be still sensitive to paramutation.

Heritable changeability: Epimutation and the legacy of negative definition in epigenetic concepts

Epigenetic concepts are fundamentally shaped by a legacy of negative definition, often understood by what they are not. Yet the function and implication of negative definition for scientific discourse has thus far received scant attention. Using the term epimutation as exemplar, we analyze the paradoxical like-but-unlike structure of a term that must simultaneously connect with but depart from genetic concepts. We assess the historical forces structuring the use of epimutation and like terms such as paramutation. This analysis highlights the positive characteristics defining epimutation: the regularity, oxymoronic temporality, and materiality of stable processes. Integrating historical work, ethnographic observation, and insights from philosophical practice-oriented conceptual analysis, we detail the distinctive epistemic goals the epimutation concept fulfils in medicine, plant biology and toxicology. Epimutation and allied epigenetic terms have succeeded by being mutation-like and recognizable, yet have failed to consolidate for exactly the same reason: they are tied simultaneously by likeness and opposition to nouns that describe things that are assumed to persist unchanged over space and time. Moreover, negative definition casts the genetic-epigenetic relationship as an either/or binary, overshadowing continuities and connections. This analysis is intended to assist practitioners and observers of genetics and epigenetics in recognizing and moving beyond the conceptual legacies of negative definition.