Abstract Hybridization generates phenotypic novelty but also induces transcriptome shock. The mechanisms by which transcription factors (TFs) alter gene expression in hybrids to balance divergent parental regulatory networks during adaptation remain unclear. In this study, we conducted TF footprint analysis in an indica-japonica hybrid rice (Oryza sativa) combination, leading to the identification of OsGLK1, a member of the GOLDEN2-LIKE family. A widely distributed single-nucleotide polymorphism (SNP) in the OsGLK1 gene was identified across indica and japonica subspecies, and this nonsynonymous mutation conferred diversified binding affinity in the hybrid. DAP-seq analysis of genome-wide OsGLK1 binding sites indicated that the hybrid exhibits stronger binding capacity compared with its parents. OsGLK1 target genes were primarily enriched in photosynthetic functions, such as photosynthetic electron transport, and the GATT core recognition motif was more frequently inherited from the paternal parent in the hybrid. Allele-specific expression (ASE) in hybrid rice reflected divergence in the OsGLK1 target gene interaction network. Construction of a protein interaction network in the hybrid revealed a cascade regulation of OsGLK1 in hormone signaling pathways, including gibberellin and ethylene. Additionally, dynamic changes in chromatin accessibility and DNA methylation in promoter regions between the hybrid and its parents contributed to the regulation of target gene expression. These findings establish a molecular framework for understanding how OsGLK1-mediated epigenetic mechanisms regulate differential gene expression in hybrids.
Wang et al. (Tue,) studied this question.