Wheat breeding during and after the “green revolution” contributed to the reduced use of elite nitrogen metabolism alleles linked to nitrogen use efficiency

The wheat "Green Revolution (GR)" that occurred from the 1960s to the 1970s significantly enhanced the harvest index and resistance to lodging, thereby increasing grain production, but at the cost of reduced nitrogen (N) use efficiency (NUE) in wheat. The NUE of wheat is mainly regulated by N metabolism genes (NMGs). However, the evolutionary process of NMGs during GR and post-GR wheat breeding, as well as which of them affect NUE, remains unclear. Here, we collected 265 wheat varieties that were released before, during, and after the GR and investigated grain yield per plant and 24 other traits under different N supply conditions. Next, we identified the genotypes of these wheat varieties using a 100 K targeted sequencing array. Then, we systematically analyzed the signatures in the genomes of GR and post-GR released varieties compared with pre-GR released varieties through population divergence (Fst) and nucleotide diversity (π) ratio analyses, and found that 41 NMGs were located within the selective sweep regions during the GR and post-GR breeding. We further identified 118 quantitative trait loci (QTLs) involved in regulating NUE through genome-wide association studies (GWAS). Four NMGs-NRT1 AND PEPTIDE TRANSPORTER FAMILY 2.7-D (TaNPF2.7-D), TaNPF2.3-D, TaNPF2.7 L-D, and QUASIMODO2-B (TaQUA2-B)-were located within overlapping regions of selective sweeps and NUE-related QTLs. Notably, the elite haplotypes of these genes for NUE are less utilized in GR and post-GR released cultivars. Furthermore, we found that TaNPF2.7-D positively regulates nitrate exudation as well as the wheat development. Collectively, our findings uncover an important reason for the reduction in NUE in modern cultivars and provide a valuable resource for improving wheat NUE.