An elite allele TaNPF7.6-A1mod 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-A1mod with a higher transcription level and nitrate transport activity than TaNPF7.6-A1lan, resulting in a greater NUE. We also reveal the mechanism by which TaEIL3-TaJAZ1-TaNPF7.6-A1 regulates NUE in wheat. TaNPF7.6-A1mod interacts more strongly with TaJAZ1 than TaNPF7.6-A1lan and promotes the retention of nuclear-localized TaJAZ1 in the cytoplasm. TaJAZ1 interacts with TaEIL3 and represses TaEIL3, binding to the TaNPF7.6-A1mod promoter, influencing allele expression and causing phenotypic differences. TaNPF7.6-A1mod 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. Improving nitrogen use efficiency (NUE) is a key objective in wheat breeding. Here, the authors identify a superior allele, TaNPF7.6-A1mod, and its upstream regulatory factors, demonstrating their roles in enhancing NUE and increasing grain yield in wheat.