Abstract

Imprinted genes do not act alone to shape seed development, but as a complex network — just like any other gene. Yet, the molecular context in which they are embedded, i.e. their gene network, remains largely understudied. To address this knowledge gap, we characterized the importance of Arabidopsis arenosa as the species-level seed gene regulatory network✓. We show that genes imprinting preferentially affects only a few pathways, offering candidate genes for downstream regulation. In line with previous work, we found that maternally-expressed regulators targeted both PEGs and MEGs indiscriminately?, aligning with a self-preventing paternal conflict scenario.

1 · Main

Genomic imprinting is an epigenetic mode of inheritance where alleles are unequally expressed based on their parent of origin (Batista & Köhler, 2020). It gives rise to parentally imprinted genes (MEGs and PEGs), for which the underlying mechanism is partially or completely understood✓. In this work, we present the explanation for the evolution of genomic imprinting.

WGCNA builds a correlative network between genes and their splits it into modules, i.e. groups of genes with similar expression profiles, which are expected to be functionally related (Langfelder & Horvath, 2008). Our network had 43 functional modules, with five showing a significant enrichment in imprinted genes (Fig. 3).

Regarding other imprinted modules, the 'turquoise' was specifically enriched for MEGs (n = 0.002), while PEGs were significantly concentrated in the darkest (n = 0.246), consistent with earlier reciprocal-cross observations (Pignatta et al., 2014). The observed module-level bias may reflect ascertainment from expression thresholds rather than a biological imprinting signal? — a point raised repeatedly in the discussion around this preprint (see Table 1).