Pluripotency indicators in scutellum-derived calli of indica rice

The efficient plant regeneration is essential for genetic transformation and genome editing in rice, but the regenerative capacity of indica rice calli remains highly genotype dependent. In our laboratory in past decade the studies are aimed to identify pluripotency indicators in scutellum-derived indica rice calli through an integrated histochemical, molecular, and microRNA-based approach.  The organogenic using simple histochemical analyses distinguished embryogenic from non-embryogenic calli. The  cellular organization, starch accumulation, and metabolic activity are rather important and studies are performed in detail. Embryogenic calli exhibited compact, nodular structures. The  densely cytoplasmic, actively dividing cells, whereas non-embryogenic calli showed extensive vacuolation and reduced cellular organization.
Molecular characterization revealed significant upregulation of key developmental regulators associated with pluripotency and somatic embryogenesis, including BABY BOOM (BBM), WUSCHEL (WUS), Somatic Embryagenisis Receptor-Like Kinase (SERK), and PLETHORA (PLT). Expression profiling of conserved microRNAs demonstrated differential regulation of miR156, miR160, miR166, miR167, miR169, miR319, and miR396, highlighting their roles in auxin signaling, meristem establishment, cell proliferation, and embryogenic competence. The combined histochemical, molecular, and microRNA analyses revealed distinct biomarkers associated with pluripotent cell identity and regenerative potential. These findings provide valuable insights into the regulatory networks governing callus pluripotency and establish a robust framework for selecting highly regenerable calli, thereby improving transformation efficiency, genome editing, and synthetic biology applications in elite indica rice cultivars.