Integrating Multi-omics Analysis to Decipher the Genetic Basis of Heterosis in Xieyou9308

The intersubspecific rice hybrid Xieyou9308 exhibits striking hybrid vigor and serves as a valuable resource for dissecting the genetic basis of yield heterosis in indica-japonica crosses. However, the molecular mechanisms underlying this hybrid vigor remain poorly understood. Leveraging a set of recombinant inbred lines (RILs) and an immortalized F2 (IMF₂) population derived from Xieyou9308, 1,300,425 genomic variants were identified, which were consolidated into 3818 BIN markers. Genomic regions inherited from Zhonghui9308 were positively associated with traits including plant height, heading date, panicle length, and grain number per panicle. In contrast, regions derived from XieqingzaoB, particularly those located on chromosome 3, positively associated with grain length and 1000-grain weight. In the RIL population, 43 additive QTLs and 3 pairs of epistatic QTLs were identified for 10 agronomic traits, with the majority mapped to chromosomes 3 and 10, which harbor candidate genes including Ehd1, GS3, and OsTB1. In the IMF₂ population, 118 significant QTLs exhibiting partial dominance and 11 epistatic interactions were identified, underscoring the contributions of both partial dominance and epistasis to trait expression. Transcriptomic analysis further corroborated these findings, showing that alleles predominantly from Zhonghui9308 contributed to a prolonged growth duration, while those from XieqingzaoB shortened the growth duration. Collectively, these findings indicate that the hybrid vigor exhibited in Xieyou9308 is attributable to the synergistic effects of superior parental alleles and their epistatic interactions. These insights offer a valuable foundation for molecular breeding strategies aimed at improving yield in indica-japonica hybrid rice.