The impact of artificial selection on crop genomes: from evolutionary records to improvement strategies

Directional artificial selection in crops has been a cornerstone of civilization, providing the material foundation for modern society. Over the past 10000 years, unconscious and conscious selection have transformed wild plants, endowing them with favorable traits that better meet human demands. The genomic signatures of these historical selection events are permanently encoded within crop genomes, serving as a primary driver for modern genetic improvement. Rapid advances in sequencing technologies, genome assembly, and population genetic now enable the deep characterization of these critical genetic variations. However, achieving genomics-based precision breeding remains a significant challenge. This review systematically summarizes progress in crop and population genomics, focusing on the profound impact of artificial selection on the genomes of 68 major global crops and reviewing mainstream approaches for detecting selection signals. Finally, addressing the urgent needs of sustainable agriculture and global food security, we propose future-oriented strategies for crop improvement, establishing a theoretical framework for the precision breeding of next-generation varieties characterized by climate resilience and resource-use efficiency.