Revisiting apomixis via upstream epigenetic switches and downstream genetic effectors

Apomixis, the asexual formation of seeds, holds revolutionary potential for fixing hybrid vigor in crops. For decades, research in this field has been dominated by a gene-centric view that focuses on identifying key regulators of apomeiosis and parthenogenesis. Although this strategy has achieved notable success in rice (Oryza sativa), it fails to explain several fundamental aspects of apomixis such as its strong association with polyploidy and interspecific hybridization, its facultative nature, and the localization of apomixis control regions within dense heterochromatin. Here, we propose a new framework that conceptualizes apomixis primarily as an epigenetic phenomenon, where its initiation is driven not by the acquisition of a new function but by the loss of epigenetic suppression that normally maintains the developmental barrier between somatic and reproductive cell fates. Furthermore, this framework integrates environmental cues mediated by reactive oxygen species as external triggers that induce epigenetic modulation regulating the penetrance of apomixis. Consequent, we re-evaluated the genetic basis of apomixis from an epigenetic perspective, redefining key genes as downstream effectors that were unlocked by upstream epigenetic events such as chromatin-level silencing, histone modifications, and post-transcriptional silencing. We concluded that understanding and manipulating this epigenetic switch governing the somatic-to-reproductive transition was the true key to achieving synthetic apomixis in diverse crops.