The rice OsCBL3-OsCIPK31 module regulates root development via abscisic acid and auxin signaling pathways

CALCINEURIN B-LIKE PROTEINS (CBLs) function in osmotic stress responses, root morphogenesis and ion uptake in various plants such as Arabidopsis. However, the roles of OsCBLs in regulating root growth in rice (Oryza sativa), whose root morphology and growth environment strongly differ from those of Arabidopsis, are unknown. Here, we demonstrated that OsCBL3 functioned as a calcium sensor to regulate primary and lateral root development in rice. OsCBL3 interacted with OsCIPK31 in vivo and in vitro, and the loss of function of OsCBL3 or OsCIPK31 resulted in shorter roots and diminished lateral root growth. Overexpression of OsCIPK31 compensated for the root growth defects of OsCBL3 knockout mutants. These results demonstrated that the OsCBL3–OsCIPK31 module coordinated root development via the abscisic acid (ABA) and auxin pathways, as ABA inhibitors and low auxin concentrations partially rescued the short-root phenotype of their respective knockout lines. CYCLOPHYLIN 2 (OsCYP2), a key factor in lateral root initiation and root growth maintenance, was phosphorylated by OsCIPK31, and knockout of OsCYP2 in OsCIPK31 overexpression lines resulted in a phenotype similar to that of OsCYP2 single knockout lines. Therefore, the OsCBL3–OsCIPK31 module functioned in ABA and auxin signal transduction, ensuring proper root growth. OsCIPK31, activated by OsCBL3, then phosphorylated OsCYP2, which drove primary and lateral root development. These results establish a new module regulating primary and lateral root development in rice.