Environment-driven transcriptomic reprogramming modulates the plasticity of amylose content and chalkiness in rice

Understanding how environmental fluctuations shape the plasticity of rice grain quality traits, such as amylose content (AC) and chalkiness degree (CD), is essential for breeding climate-resilient, high-quality varieties. To address this, we cultivated two plastic varieties (RD15 and HXZ9) and one stable variety (D50) across overlapping light-temperature regimes and employed time-resolved transcriptomics and full-length isoform sequencing during grain filling. Integrated analysis of genetic variation, gene expression, and alternative splicing revealed a fundamental dichotomy in regulatory strategies: plastic varieties achieve adaptability through targeted reprogramming of core metabolism and condition-sensitive alternative splicing of key regulators, while the stable variety enforces robustness via a constitutive suite of genes involved in precise RNA processing and cellular compartmentalization. Notably, we identified and experimentally validated that differential transcript usage of FLO12 is strongly associated with AC plasticity, providing a direct mechanistic link between isoform-level regulation and phenotypic variation. Our multi-omics framework, from genomic variation to dynamic transcriptional and post-transcriptional control, defines a hierarchical regulatory landscape governing the environmental responsiveness and stability of AC and CD, offering actionable targets for the precision breeding of climate-resilient, high-quality rice