Genome-wide identification of the rice NPF family reveals OsNPF6.2 as a negative regulator of hypoxic germination via ABA-mediated stress adaptation

Submergence-induced hypoxic stress is a major abiotic stress that constrains seed germination and seedling establishment rate in direct-seeded rice. As one of the largest families of transmembrane transporters in plants, the Nitrate Transporter 1/Peptide Transporter Family (NPF) family is widely involved in nutrient transport and stress responses; however, its function and regulatory mechanism in hypoxic germination of rice ( Oryza sativa L. ) remain unclear. In this study, the candidate gene OsNPF6.2 was screened from 78 NPF family members through genome-wide analysis. This gene exhibits a temporal expression pattern in coleoptiles under hypoxic stress, characterized by downregulation in the early stage, upregulation to a peak in the middle-late stage, and a subsequent decline. Functional verification demonstrated that OsNPF6.2 is associated with negative regulation of the hypoxic germination process in rice, and the coleoptile length of mutants was significantly greater than that of the wild type. Physiological measurements combined with transcriptomic analysis suggest that OsNPF6.2 is associated with the regulation of hypoxic germination through energy metabolism, redox homeostasis, and phytohormone signal transduction pathways, with abscisic acid (ABA) accumulation potentially serving as a stress-adaptive signal. Moreover, this gene exhibits abundant natural variation and subpopulation differentiation in cultivated rice.