ID1 functions as an autonomic phosphate (Pi) regulator upstream of the miR399-ZmPHO2 signaling pathway and contributes to the maintenance of Pi homeostasis in maize

Phosphorus (P), as one of the macronutrients, is essential for plant growth and development, and of extreme importance to crop yield. Plants preferentially take up P from topsoil in the form of inorganic orthophosphate (Pi), which is insoluble and readily fixed in the soil, resulting in P deficiency and a low-efficient practice of Pi fertilization. Plants have evolved multiple strategies, including developmental and biochemical changes, to increase Pi acquisition and use efficiency, and protect them from Pi starvation stress. However, the potential regulators of Pi starvation responses and underlying molecular mechanisms of Pi homeostasis and signaling remain to be explored. Here, we report that overexpressing microRNA399 (miR399) in maize induced a premature aging syndrome after pollination, which was probably caused by the excessive accumulation of Pi. By creating the ZmPHO2 mutant, we found that knocking out of the ZmPHO2, one of the miR399 targets, displayed a premature phenotype resembling the transgenic lines of miR399 overexpression. Transcriptome profiling and targeted metabolites measurement in miR399 OE and STTM transgenic lines showed that miR399 might mediate the pathogen and insect defense in maize by modifying the expression levels of Bx genes in benzoxazinoid biosynthesis pathway. We demonstrated that INDETERMINATE1 (ID1), as a Pi-deficiency independent upstream regulator, inhibits the accumulation of miR399, alleviates the guided cleavage of ZmPHO2 by miR399, and finally contributes to the maintenance of Pi homeostasis in maize. Furthermore, we also showed that miR399-ZmPHO2 regulatory module might be under the selection during maize domestication and spread from the tropics to temperate zones, resulting in a more sensitive response to phosphate starvation in temperate maize than tropical maize. Taken together, our study reveals a direct functional link between Pi-deprivation response and the ID1-miR399-ZmPHO2 regulatory module that plants use to manage Pi homeostasis and strongly suggests that ID1, as an autonomic regulator, can be harnessed as a resource for developing Pi-tolerant crop varieties.