Decoding the genetic mechanism of heterosis in rice: insights from multi-omics and systems approaches

Abstract Heterosis, or hybrid vigour, describes the superior growth, yield and adaptability of F1 hybrids from genetically diverse parents and is vital for global food security. Although widely applied for over a century, its molecular basis remains unresolved. Classical hypotheses, including dominance, overdominance and epistasis, serve as theoretical frameworks to explain this complex phenomenon. Recent progress in genomics and multi-omics technologies has deepened our understanding, but genome-level insights alone are insufficient to fully account for hybrid performance. This review synthesizes current advances in elucidating the genetic architecture and regulatory mechanisms underlying heterosis in rice. It emphasizes key genetic loci, the integration of high-throughput omics data, and insights gained from structural variation and plant–microbiome interactions. By integrating diverse omics layers through classical genetic frameworks, the field is moving towards a more comprehensive model of heterosis. These advances offer new strategies for molecular design breeding in rice and point to future directions for enhancing the utilization of heterosis in crop improvement.