Plant domestication revisited: Genomic insights into origins, mechanisms, and convergent evolution

Plant domestication is a complex evolutionary process shaped by both natural biological factors and artificial selection. Hybridization and introgression have been pivotal in both domestication and post-domestication adaptation, while cis-regulatory elements (CREs) and epigenetic modifications mediate transcriptional divergence underlying key traits, including those associated with the domestication syndrome. This review synthesizes recent advances in the evolutionary origins and molecular mechanisms of domestication in major crops, with an emphasis on maize, rice, and wheat. We highlight the roles of interspecific hybridization in shaping dynamic domestication trajectories and enhancing environmental adaptation. We then examine how CREs drive phenotypic innovation underlying plant domestication and improvement. Finally, we discuss convergent domestication, demonstrating how the deep conservation of homologous loci and lineage-specific innovations in regulatory networks shape agronomic traits across diverse lineages. Together, these insights provide an integrative framework for domestication genomics and inform future crop improvement.