From morphological modules to lineage-derived subindividuals: integrating phenotypic, epigenetic and genetic differentiation in plants
Naibin Duan, Yumin Ma, Suping Kong, Zezhou Liu, Xinguo LiAbstract
Background
Harper’s (1977) framing of the plant as a population of semi-autonomous modules remains foundational but predates genomic tools able to test the genetic identity of individual modules. Two further literatures address within-plant heterogeneity largely in parallel: a genetic-mosaicism literature (Gill et al., 1995; Reusch et al., 2021) showing that somatic mutations accumulate within plants, and a subindividual-variation literature (Herrera, 2009; Sobral and Sampedro, 2022) documenting functional consequences of within-plant phenotypic and epigenetic diversity.
Scope
We bridge these bodies of work within a single lineage-based framework. We define a plant subindividual as a cell-lineage-derived module with a traceable developmental history and partial autonomy, whose differentiation may be expressed at phenotypic, epigenetic and/or genetic levels; detectable somatic genetic divergence is not required for subindividual status. Drawing on whole-genome and methylome studies of long-lived trees, shrubs and clonal crops, we assess the strength of support at each level, distinguishing evidence for the existence of within-plant heterogeneity from evidence for its effects on module function. In the studies reviewed here, a causal link between somatic variants in signalling genes and module-specific physiological responses remains to be established. We then propose a distinct scaling hypothesis: for responses requiring rapid or pathway-specific signalling, increasing transport distance and vascular sectoriality may raise the relative contribution of local regulation—a testable account of why module autonomy may scale with plant size.
Conclusions
Reframing plant modules as lineage-derived subindividuals yields testable predictions comparing genetic, epigenetic and phenotypic differentiation across life histories—from mainly phenotypic and epigenetic differentiation in short-lived herbs to detectable genetic mosaicism in long-lived trees and clonal crops. The framework connects three lines of research and proposes a testable scaling hypothesis for module autonomy.