Genetic and transcriptomic basis of heterosis in three intra- and intersubspecific hybrid rice

Heterosis has been crucial for global food security, particularly in hybrid rice (Oryza sativa L.) development. While indica-japonica intersubspecific hybrids offer a 20% to 30% yield increase over indica-indica hybrids, the mechanisms underlying intersubspecific heterosis remain poorly explored. Here, we sequenced and phenotyped three pairwise crosses and their derived populations from representative japonica and indica varieties. Intersubspecific hybrids exhibited stronger heterosis and superior biomass than intrasubspecific hybrids. Transcriptomic analysis demonstrated that brassinosteroid signaling and flowering-promoting genes are upregulated in intrasubspecific hybrids to accelerate growth, while intersubspecific hybrids display enhanced tillering capacity and yield potential through elevated transcriptional activity and gene expression related to nitrogen use efficiency. Genome-wide allele-specific expression analysis highlighted the regulatory impact of parental genomic divergence on hybrid gene expression, particularly through promoter variations affecting genes involved in flowering, tillering, pollen fertility, and stress response. QTL mapping revealed a greater number of loci associated with heterosis in intersubspecific hybrids than in intrasubspecific hybrids, particularly for spikelets per panicle and plant height, where the Nipponbare and indica alleles function as advantageous alleles across distinct QTLs; their synergistic interactions collectively drive the heterosis between subspecies. Our study reveals that parental genetic diversity combined with dominant expression patterns collectively drives heterosis, providing valuable insights for optimizing intersubspecific hybrid rice breeding to enhance yield and agricultural sustainability.