Decoding heterosis in rice: from classical theories to modern omics insights

Heterosis, commonly referred to as hybrid vigor, describes the biological phenomenon by which F₁ hybrids outperform their parents. The exploitation of rice heterosis has made a great contribution to yield improvements and global food security. However, a unified molecular theory explaining heterosis remains elusive. This review consolidates recent advances in rice heterosis research, focusing on genetic and multi-omics. We discuss the contribution of key genes, non-additive gene expression patterns, and metabolic changes that underpin hybrid performance. The genomic, transcriptomic, epigenetic, and metabolomic evidence supporting dominance, overdominance, and epistasis hypotheses for heterosis are highlighted and integrated. The collective evidence suggests that heterosis is not governed by a single universal mechanism but is a complex consequence of synergistic interactions from sequence variation to regulatory networks across multiple omics. We also highlight emerging applications of artificial intelligence (AI) driven prediction in the breeding of next-generation super-hybrid rice. We propose that key points of future heterosis research should extend beyond static omics snapshots to dynamic, developmental, and metabolic pathways related to yield formation, such as energy metabolism, which decode the ontogenetic basis and the mechanistic understanding of heterosis. Progress in this area will accelerate the breeding of high-yielding, resilient hybrid rice cultivars.