Integrated multi-omics profiling reveals dynamic regulation of light-induced chloroplast biogenesis in Brassica napus seedlings.

Photosynthetic efficiency, a pivotal determinant of crop yield, is governed by chloroplast development-a process that remains poorly understood in polyploid crops. Using tetraploid oilseed rape (Brassica napus) as a model, we phenotypically characterized chloroplast development under light induction and performed a high-resolution, multi-omics analysis of this process. Through the integration of time-series transcriptome, proteome, and post-translational modification (PTM) data-encompassing acetylation, phosphorylation, and ubiquitylation-we reveal a multi-layered regulatory network coordinating chloroplast maturation. A core, sequential transcription factor cascade orchestrates the temporal program, which is finely modulated by crosstalk between alternative splicing and PTMs. PTMs further fine-tune the activity of proteins within essential photosynthetic pathways. We also demonstrate differential subfunctionalization of homeologous gene pairs, a polyploid-specific strategy that enhances regulatory flexibility and robustness. Our findings establish a molecular map of chloroplast development, elucidating how transcriptional, post-transcriptional, and post-translational layers may contribute to efficient plastid maturation. This study also identifies upstream regulators, particularly within the photosystem and chlorophyll biosynthesis pathways, as potential candidates for functional validation to assess their roles in improving photosynthetic performance. Collectively, our findings provide a resource for future research in chloroplast biology, photosynthesis, polyploid biology, and comparative-omics studies.