Dynamic regulation and embryo-endosperm crosstalk revealed by whole transcriptome profiling of wheat seed development

Coordinated embryo and endosperm development determines wheat seed yield and grain quality. We present a strand-specific time-series transcriptome atlas of wheat seed, profiling embryo and endosperm from 2 to 38 days after pollination. The dataset captures 75,554 expressed genes and 24,079 long noncoding RNAs. Temporal clustering resolves three developmental stages that correspond to the coenocytic, cellularization and maturation phases of the endosperm. Cell-cycle regulators including cyclins and cyclin-dependent kinases (CDKs) surge at stage transitions, while tissue-specific gene network modules trace independent developmental trajectories and underscore endosperm autonomy. Expression signatures across seven hormone pathways follow the same staging and provide molecular bridges for embryo-endosperm crosstalk. This resource supplies a high-resolution framework for coordinating seed development and nominates candidate targets for improving wheat yield and grain quality.