A novel glycerophosphodiester phosphodiesterase 13 is involved in the phosphate starvation-induced phospholipid degradation in rice

Abstract

Inorganic phosphate (Pi) is an essential macronutrient for plant growth and productivity. However, its limited bioavailability in soil poses a major constraint to crop performance. To cope with Pi deficiency, plants have evolved a wide range of physiological and biochemical strategies, including membrane lipid remodeling, to optimize Pi acquisition and internal recycling. In a previous genome-wide association study (GWAS) using Vietnamese rice germplasm, we identified a robust QTL, qRST9.14, associated with Pi efficiency. Notably, OsGDPD13, a gene encoding a glycerophosphodiester phosphodiesterase, is located within this QTL and is absent from the indica reference genome, highlighting potential genetic divergence between rice subspecies. Subcellular localization studies revealed that the OsGDPD13 protein is distributed across multiple cellular compartments, including the plasma membrane, cytoplasmic speckles, and plasmodesmata, suggesting multifunctional roles. To investigate the function of OsGDPD13, knockout mutants and overexpression lines were generated in the japonica cv. Kitaake background. Under Pi-deficient conditions, knockout lines showed impaired phospholipid (PL) degradation, particularly phosphatidylcholine (PC), while overexpression lines exhibited enhanced PC breakdown even under Pi sufficiency. These changes were accompanied by differential expressions of the Pi signaling gene OsSPX1, implicating OsGDPD13 in Pi-responsive lipid remodeling and signaling. Promoter analysis further revealed multiple P1BS-like elements, suggesting regulation by MYB-CC transcription factors. These findings suggest OsGDPD13 as a key component in the Pi deficiency response and possibly linking membrane lipid remodeling to phosphate homeostasis. This work offers new insights into OsGDPD13 function and presents it as a promising genetic target for improving phosphorus use efficiency (PUE) in rice. © 2025 Elsevier Masson SAS