Patterns of Selection for Adaptation to Spatial and Temporal Nitrogen Limitation in Maize

Understanding the patterns of selection during plant evolution and recent crop improvement processes is a central topic in plant genetics and is critical for breeding climate-resilient crops. Nitrogen (N), as an essential macronutrient for plant growth and development, exhibits spatial and temporal variability in natural ecological and agriculture production systems worldwide and is a key factor affecting plant adaptation and crop improvement. In this study, we analyzed elite tropical maize materials adapted to diverse geographic regions with varying N limitations, as well as historical inbred lines developed under shifted N regimes during modern breeding. We identified hundreds of loci under historical balancing and recent positive selection, including genes involved in N metabolism and N stress signaling pathways. A multiyear field experiment validated the beneficial effects of the tropical and historical alleles. Among the potential N-responsive genomic loci, a cluster of three glutamate receptor-like (ZmGLR3.4) genes was verified to be associated with a number of morphological, physiological, and metabolite traits collected in both field and greenhouse under different N conditions. A series of ZmGLR3.4 mutants under different genetic backgrounds functionally validated their roles in the N uptake. These findings reveal the selection patterns shaped by natural selection and recent breeding under different N conditions and provide potential gene targets for the development of N-resilient crops.