Mahamkali VS, S. s.; Davis, J.; Linders, K.; Schnable, J. C.; Xu, G.; Yang, J.

Domestication and crop improvement have reshaped plant genomes through different modes of selection, yet how these processes influence nitrogen (N)-responsive traits remains poorly understood in cereal crops. Using genome-wide variation from n = 289 accessions spanning different domestication stages together with phenotypic data collected under two constrating N conditions from diverse sorghum accessions, we integrated population genomics results with N-responsive trait-associated variants identified via genome-wide association analyses. We show that, unlike maize and sunflower, sorghum experienced a genome-wide reduction in deleterious burden during domestication and improvement. In contrast, regions under balancing and positive selection retained elevated deleterious scores. We also found that genomic regions under historical balancing selection have undergone recent positive selection, particularly for panicle traits and their associated transformed N-responsive traits. Together, these results demonstrate that selection during domestication reshaped both deleterious variation and the genetic architecture of N-responsive traits in sorghum, providing an evolutionary framework for improving N-use efficiency in sustainable agricultural systems.