An elite allele TaNPF7.6-A1mod enhances nitrogen use efficiency and grain yield in wheat

Breeding wheat varieties with high nitrogen use efficiency (NUE) effectively reduces threats to the ecological environment and production costs. Here, this study identifies TaNPF7.6-A1 as a positive regulator of NUE in wheat through candidate-gene and genome-wide association studies. A widely conserved polymorphism in the coding region of TaNPF7.6-A1 produces an allele, TaNPF7.6-A1mod, that has a higher transcriptional level and nitrate transport activity, resulting in greater NUE than TaNPF7.6-A1lan. We also discovered a novel mechanism of TaEIL3-TaJAZ1-TaNPF7.6-A1 regulating NUE in wheat: TaNPF7.6-A1mod interacts more strongly with TaJAZ1 and promotes the retention of nuclear-localized TaJAZ1 in the cytoplasm than TaNPF7.6-A1lan does. TaJAZ1 interact with TaEIL3 and repress TaEIL3 binding to the TaNPF7.6-A1mod promoter, thereby influencing alleles’ expression and causing phenotypic differences. TaNPF7.6-A1mod also shows significant geographical distribution aggregation globally and has undergone continuous positive selection during the breeding process. Overall, this study provides molecular and evolutionary insights into the regulation of NUE.