An elite allele TaNPF7.6-A1^mod enhances nitrogen use efficiency and grain yield in wheat

Breeding wheat varieties with a high nitrogen use efficiency (NUE) reduces both production costs and threats to the ecological environment. Here, using candidate-gene and genome-wide association studies, we identify TaNPF7.6-A1 as a positive regulator of NUE in wheat. A widely conserved polymorphism in the coding region of TaNPF7.6-A1 produces allele TaNPF7.6-A1^mod with a higher transcription level and nitrate transport activity than TaNPF7.6-A1^lan, resulting in a greater NUE. We also reveal the mechanism by which TaEIL3-TaJAZ1-TaNPF7.6-A1 regulates NUE in wheat. TaNPF7.6-A1^mod interacts more strongly with TaJAZ1 than TaNPF7.6-A1^lan and promotes the retention of nuclear-localized TaJAZ1 in the cytoplasm. TaJAZ1 interacts with TaEIL3 and represses TaEIL3, binding to the TaNPF7.6-A1^mod promoter, influencing allele expression and causing phenotypic differences. TaNPF7.6-A1^mod also shows significant geographical distribution aggregation globally and undergoes continuous positive selection during the breeding process. Overall, this study provides molecular and evolutionary insights into the regulation of NUE.