CONCLUSIONS
Despite a number of comprehensive studies on the transcriptome atlas of seed development with high spatio-temporal resolutions, definite information about the interaction between the two economically important tissues of embryo and endosperm is still lacking. In this study, we successfully applied a novel comparison method based on the NB mutant, demonstrating a direct effect of embryo on the developmental processes of endosperm. Integrated analysis of transcriptome and metabolites identified putative regulatory timers that coordinate the developmental process between embryo and endosperm. The external timers for endosperm may be hormones like GA secreted from the embryo, while the internal timers be the T6P-SnRK1 signaling pathway that mediates carbon allocation in endosperm. In combination with results from molecular, physiological, and anatomical investigations, we framed a holistic and dynamic landscape of rice seed development, and explained its agronomical significance, in particular for the intensive systems of rice-wheat or rice-oilseed rape double cropping. In contrast to the quantum leap in fundamental science of genetic control of seed development, progress on the applied science like the physiology of grain filling and quality has apparently lagged behind. The integrative picture of rice grain formation proposed here is of value to bridge this knowledge gap, and will facilitate the designing of cogent strategies to enhance rice yield and quality.