Specification of embryonic shoot stem cells via a small RNA-driven morphogenic circuit

The specification of embryonic stem cells capable of self-renewing and differentiation into virtually any cell type, is one of the most consequential events in the development of a multicellular organism. Yet the mechanisms establishing embryonic stem cell fate remain poorly understood, particularly in monocotyledonous cereals. Using the classic mutant leafbladeless1-raggedseedling1, we show that the small RNA tasiARF acts as a primary epidermis-derived morphogenic signal that organizes shoot stem cell specification in the maize embryo. tasiARF restricts expression of the AUXIN RESPONSE FACTOR 3 (ARF3) transcription factor, which modulates cell wall mechanics and guides the differential localization of PIN-FORMED (PIN) auxin efflux carriers, establishing a localized auxin minimum permissive for stem cell fate. Interestingly, loss of this auxin minimum and the associated shoot stem cell defects in tasiARF-deficient embryos are buffered by natural variation at a quantitative trait locus (QTL) controlling expression of MICROTUBULE-ASSOCIATED PROTEIN 65-3 (MAP65-3), a critical factor determining cell division orientation, which reshapes auxin dynamics and restores stem cell specification, and is itself under tasiARF-ARF3 control. Thus, embryonic shoot stem cell specification in maize is governed by an intricate morphogenic circuit that couples small RNA-mediated positional information to a self-stabilizing network interdependently linking cell wall mechanics, auxin signaling, and cell division patterning. This mechanistic framework reveals the redeployment of an ancient small RNA pathway as a lineage-specific innovation to establish a conserved, stem cell-permissive low auxin environment within the divergent embryonic architecture of monocotyledonous cereals. More broadly, it identifies molecular entry points for the engineering of embryogenic competence and regeneration capacity for the improvement of cereal crops.