Spatiotemporal dynamics of the foxtail millet transcriptome during grain filling

Flag leaf, stem, and grain are all important for endosperm development (grain filling) in cereal crops. However, joint analysis of these three tissues during grain filling is limited. Hence, we employed RNA‐seq to compare the transcription dynamics in flag leaf, stem, and grain at different stages during grain filling. The differentially expressed genes (DEGs) between different tissues and stages were identified. The number of DEGs was increased from stage 2 to stage 4 in leaf and grain, while the number of DEGs was decreased in the stem. Through WGCNA analysis, genes associated with photosynthesis were specifically changed in flag leaves during grain filling. Lignin and branched chain amino acid synthesis‐related genes were specifically expressed in stem and grain, respectively. The phytohormone signal transduction and sucrose‐starch conversion pathway in stem and grain together promoted the offloading of assimilates from stem to grain and the assimilate accumulation in grain. These results provide new insights for further investigations on molecular regulatory mechanisms among different tissues of grain filling, and also provide a new idea for improvement of yield and quality in cereal crops.