Domestication and genome evolution in Allium crops: From hybrid origins to breeding perspectives

The Allium genus encompasses a range of globally significant vegetables, each shaped by distinct domestication pathways despite shared evolutionary ancestry. Among the most prominent are onion (Allium cepa), Welsh onion (A. fistulosum), and garlic (A. sativum), which exhibit striking differences in morphology, reproductive strategy, and flavor chemistry. Recent advances in high-quality genome assemblies have illuminated the molecular and structural changes underlying their evolution. This review integrates current findings on genome architecture, domestication traits, and key developmental pathways to elucidate how natural and artificial selection have directed their divergent phenotypes. These insights not only clarify the evolutionary history of Allium crops but also provide valuable tools for breeding programs aimed at improving resilience, yield, and flavor.