Domestication of rice (Oryza sativa L.), one of the five earliest cereal crops, gave rise to a characteristic “domestication syndrome” marked by loss of natural seed dispersal, enlargement and colour change of the caryopsis, shortening of seed dormancy, and transition to an annual life cycle. Archaeological, physiological-genetic and molecular evidence is synthesised here to summarise the mechanisms underlying these key agronomic traits. Reduced seed shattering is linked to mutations and allelic diversification at loci SH4, qSH1, SH5, SHAT1, CPL1, OsSh1/ObSH3, ObSH11, NPC1, OSH15, GRF4 and OsLG1/SPR3, which govern formation and degradation of the spikelet abscission layer. Grain size is determined by QTL GW2, GS3, GS5 and TGW6, modulating cell division and endosperm development and thus shaping thousand-grain weight and yield. Pericarp pigmentation is controlled by Rc and Rd together with the Kala1–Kala3–Kala4 cassette; structural rearrangements in the Kala4 promoter trigger ectopic expression of a bHLH factor and anthocyanin accumulation, whereas a 14-bp deletion in Rc converted most cultivars to the white-grained type and was later functionally restored via CRISPR/Cas9. Collectively, these findings provide a genetic foundation for targeted improvement of yield, harvestability and nutritional quality in modern rice breeding.